Calling them “prefixes” is about the total of the confusion. Call them “instances” or even just “boxes” and it’s suddenly clear what they do.
(The only reason I’m not using “sandbox” is because they don’t really provide sandboxing from a security point of view, only a kind of separate instance with its own configuration but with access to everything via the Z drive)
Once you figure out that using a different “wine prefix” only really means a separate “Windows” with it’s own config and file structure there’s nothing confusing about it.
Same. However some mod programs that rely on Windows prerequisites like C++ and .NET don’t have that (which is where my frustrations were stemming from)