I'd probably go with a "kitchen" metaphor here.
The executable for a program is a list of instructions for the CPU to execute. Windows and Linux gaming machines will usually use x64. Most of the instructions are logic eg. how to add numbers together, what comparisons to make, what to copy from one place to another; and they're exactly the same on both Windows and Linux, you can run them as-is.
Some instructions ask the operating system to do things, like open a file to read. Windows and Linux do these quite differently, but you know how one works then you can change it to the equivalent ask for the other machine. Making the translation takes a moment, but some things are faster on Linux than Windows, so it's not very easy to generalise as to whether it'll be faster overall to do certain things. The really important operating system calls for games tend to be messages to pass to the GPU, and the Proton team have put a lot of work into making these as fast as possible.
If you think of it like following a food recipe, then given the ingredients you'd expect that most people would produce exactly the same meal by following it. Most of the steps will be exactly the same for everyone. However, if a step requires a piece of equipment that you don't have, then it might take longer to follow the recipe if you've got to make do with different stuff. Similarly, you might be able to prepare things quicker if you've got a whole pile of restaurant-level gear and can do some of the steps differently.