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To be honest, it is quite complicated now as well with all of the proprietary software
(sh.itjust.works)
I use Arch btw
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Config files that are meant to be used as sane defaults for new user accounts, yes. Config files that are meant to be manually edited, no.
Besides, there are a lot of examples of configs that are saved in ProgramData, like, let's say, registration info for proprietery programs (of course, this info needs to be shared amongst users, so your safest bet is ProgramData). Hidden by default, makes it perfect for storing everything the program is trying to hide from the user.