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As you noted, it appears to be both, at least in terms of the computer systems.
Jett Reno noted that the warp plasma conduits were being replaced with polaric warp conduits, so I assume there was a total physical refit, albeit one thats very backwards compatible when it comes to archaic computer systems.
I see it as similar to what would happen if a viking longboat suddenly appeared in modern times with a crew that decided they'd like to become part of their country's navy. Assume for sake of argument that this viking longboat is endowed with a magical stave that allows it to instantaneously transport itself to whatever point on the globe the captain chooses. This magical stave is imprinted on the hull of the boat itself and cannot be removed or transferred.
We would re-enforce the wooden hull of the boat with steel. No doubt a nuclear reactor would be far too massive and complex, so we would likely install gas turbine engines, or perhaps maybe even an electrical propulsion system, space permitting. Radar systems would be installed, but we couldn't use a phased-array radar system; it's dependent on the geometry of the ship's superstructure. There wouldn't be room for a vertically-launched missile system, but an older deck-mounted missile launch system would certainly be possible. A 20mm deck gun would work just fine, but sea-based artillery is out of the question. A 5-inch gun requires far too much supporting equipment below decks. Communications would be no problem; install a mast on the newly steel-reinforced deck and place a small-ish transceiver somewhere, and the boat now has the same high-bandwidth comms afforded to modern ships.
Computing power would be somewhat of a problem. Modern ships rely on large spaces full specialized military-grade purpose-built computing systems. We could likely fit a server rack with a few high-powered Xeon servers somewhere on the ship, but it wouldn't have the same total-ship integration that something like an Aegis cruiser or destroyer has. Processing power might be the same (if not better), but the overall topology of the system would be vastly different, and likely more limited in what sort of inputs the ship's "main computer" is able to receive and process.
I would suspect that a 23rd century starship in the 32nd century would be in a very similar scenario. As long as the ship is still considered spaceworthy, many modern advancements could be installed or easily modified to fit the 900-year-old ship. Because the unique capabilities of the USS Discovery are inextricably tied to the ship itself and it's crew, however, there will always be limitations on what technology can be installed without altering the structure of the ship to the point that the spore drive no longer functions. That's part of the reason why I think the spore drive in the Discovery and a magical stave on a viking longboat are a good comparison. Both have "magical" elements and may or may not rely on the ship itself being set up in such a way to allow these magical elements to function. Change the ship too much, and it's no longer the same ship.
That does bring up an interesting argument regarding the Mk2 spore drive that was used on Booker's ship. If there is a way to create a spore drive that can be operated on any modern starship, is there really any reason for the 900-year-old Discovery to still be in active service? Seems to me that a 32nd-century starship with Stamets onboard would serve the same function, only better.
Interesting point of comparison with the longboat, although it is also worth pointing out that there would be inherent weaknesses in the design that would make it unsuitable for fitting modern equipment to, having been designed for different forces and standards.
That does bring up an interesting argument regarding the Mk2 spore drive that was used on Booker's ship. If there is a way to create a spore drive that can be operated on any modern starship, is there really any reason for the 900-year-old Discovery to still be in active service? Seems to me that a 32nd-century starship with Stamets onboard would serve the same function, only better.
Yes, but arguably more for the crew/Zora than anything. All but a tiny handful of the crews are from the deep, ancient past. Their ability to use modern technology of the 32 century varies. Michael might be fine, having spent a year needing to adapt, but the others could struggle.
Discovery was refitted with that in mind, its systems overhaul keeping to a more familiar 23rd century template.
Otherwise, excepting Stamet's expertise, they don't really need it, besides not wanting to waste resources overhauling and immediately retiring the ship. 32nd century computers would almost certainly be able to more easily overcome the computing limitations that prevented a fully computerised spore jump in the 23rd century.
I've always had a fan theory that navigating the mycellial network requires that the navigator be a conscious entity for one reason or another. It explains why there was so much trouble with development in the first place. If that's true, you could argue that no matter how advanced 32nd century computers are, they still won't be able to calculate a spore jump. Starfleet seems opposed to the idea of a sentient AI in any era, so that leaves Zora as the only "computer" that could operate the spore drive without a flesh-and-blood navigator. That would explain some of why the Discovery is still in service.
Also, we've seen on screen that the navigator must have some kind of connection to nature and/or the fabric of the universe itself. Stamets had the tardegrade DNA, and Booker had his species' unique abilities. I'm not sure anyone else fits this role, excepting the obvious like Q or the Travellers, who would have no use for it in the first place.
I've always had a fan theory that navigating the mycellial network requires that the navigator be a conscious entity for one reason or another.
Having a conscious navigator is highly beneficial, but isn't a necessity. Discovery was able to perform spore jumps prior to that, it's just that their range was limited, as their computers were not powerful enough to make the calculations required for longer jumps.
Starfleet seems opposed to the idea of a sentient AI in any era, so that leaves Zora as the only "computer" that could operate the spore drive without a flesh-and-blood navigator.
I wonder if Zora could. They may be conscious, but they are still a computer, and might lack the intuition required for mycelial travel by virtue of not being biological.
That would explain some of why the Discovery is still in service.
It would. But as someone else pointed out, Discovery is currently housing several time-displaced humanoids from the 23rd century, and a sapient comouter. Evicting them might be more unethical than letting them continue piloting a comparatively ancient starship, especially if they can refit it to something close enough to modern starship performance.
It might no longer be the bleeding edge starship that the Crossfield used to be, but it also doesn't need to be.
Also, we've seen on screen that the navigator must have some kind of connection to nature and/or the fabric of the universe itself.
I'd disagree there, and say that it seems it be more due to needing a way to commune with the spores to make it work.
Humans can't do that, so Stamets is only able to do that using the Tardigrade DNA, mimicking the connection that it had with the mycelial spores. By comparison, Book could tap into his empathic abilities to the same end, and wouldn't need that kind of modification.
Although it does raise the question of how much of the Mycelial network navigation is due to the navigator, how much is due to the drive itself, and how much is due to the spores/network itself doing things in response to the intent communicated by the navigator.
Logically, any other species that could communicate with the spores in one way or another would also be able to take starships on the same journey, even if their way of communicating with the spores is different to that of Book or Stamets.