Intriguing. After some testing, FFA works with revision 409 of the gametypes file, and NOT 411. Also, it does NOT work with SpectatorESP (turned out to be the major culprit I believe, more testing when I'm back home and not on laggy RDP). sv_pure does not have an impact. Hip hip hooray for CSSDM FFA!!!
EDIT: Btw, any news on the possibility of having the radar disabled/scrambled while in FFA?
EDIT2: Another btw, the bot quotas still did not work on a mapchange of an empty server, and I figured out why. The plugin would set the bot_quota, then the server would load the server.cfg (which has the bot_quota 0). I fixed this by placing bot_quota 0 in autoexec.cfg instead of server.cfg, and voila!