Solution: Posting this in case someone else runs into this problem.
Apparently the simple explanation is that Moonlight can only read one configuration file. So the solution was
copy the controller config strings of both controllers into one single .map file.
in the global.conf set both controllers to use the same .map file (where all controller mappings are stored)
So my global.conf now looks like this:
# global config file for moonlight
input = /dev/input/event0
mapping = /home/pi/msigc302.map
input = /dev/input/event1
mapping = /home/pi/msigc302.map
quitappafter = true
