That manual is written by Jordan, but the key point is not the manual, it's the software and protocol.
JS8Call has a few bits it can devote to "special" group calls that save a lot of bandwidth, and saving bandwidth improves how much you can send in a single cycle, improving both communication speed AND fidelity. But there are only a few of them because they are limited by the protocol design, so Jordan necessarily has to be selective. He chose to devote one of those to a group with christofascist and insurrection ties. That is an implied endorsement, or special assistance rendered to that group that turns off a LOT of hams. It's quite literally baked in to the software. If that doesn't bother you, fine, but I hope you can see why many of us would rather just stay clear of something like that.
The relaying is also a problem. Though most people don't automatically relay, it's worth being aware that if you turn that feature on, you could be carrying water for AMRRON. It could also be illegal at a point. Without the network features of JS8Call, it doesn't actually bring a while lot of fancy features beyond existing digimodes.
Yes. This is a setting in the menu. Audio source is selectable separately for -D and non-D, so one of them can use the mic and one can use the aux, or whatever you want. I believe it also recalls the various DSP settings as well, so you can set things up how you like for phone, and for digi and easily toggle back and forth.
It's not about a pre-set per-se, but about having 2 custom U/LSB profiles.