Yes, python does have its own concept of where modules are to be stored. However, in order to separate out an application like MMA from the rest of the riffraff I like to have it separate
One problem with storing application specific modules in /lib/python* is that you do need root permission to get there ... so then you need to use user-write space ... and, besides, this is the way I started the mess
Having config files in .config is a good idea. I've added environ.get('HOME')+'/.config/mma/mmarc' into the search path at line 113 in paths.py and added "from os import environ" in the header. Do you know if there is an equivalent for mac and windows? BTW, the first mmarc is the only one processed. So, it's easy to have a directory specific file ... in that case I usually start it with an include statement.