The 'user' mod, from #1940, is intended to be an always-writable location for, in particular, atlas maps, and other user data.
It is not really a 'mod', since it doesn't have a a mod.json and can't be 'not loaded' (NB: there is a command line flag, but that's hacky at best).
The problem of knowing where to write files is difficult. See https://code.wildfiregames.com/rP13472#43581
Given that we can have many mods loaded, we can write to a bunch of different locations (/ with D3217, we'd write to the highest priority mod). This is not necessarily obviously better, given that a map made with multiple mods might not be particularly compatible with only one mode.
Ergo, I'd suggest keeping this 'user' mod, but moving it ouf of 'mods', and into '[userpath]/userdata'. This makes it less weird, and removes one name from there.
The concept of "dev copy" should probably be reworked, possibly having a configure option to activate it for modders would be useful.