As of now (today's update), settings for different resolutions do not require separate files (such as faction1024x768.ini) and entries in resolutions.lst. Instead, all keys for different resolutions are in faction.ini, and keys for different resolutions require "resolution x y" line preceding them.
Example:
#default keys start
key1=100
key2=200
...
#default keys end
resolution 800 600
# 800x600 keys start
key1=150
key2=220
...
# 800x600 keys end
resolution 1024 768
# 1024x768 keys start
key1=1000
key2=2200
...
# 1024x768 keys end
See current ini file (in factions002.zip) for reference.