True. Though those controls were a part of nightly, so unfortunately it didn't matter if they were in any mod or not yet, because there was a bug in the SCP code that enabled all controls by default even though I had specifically set the controls to not be enabled by default to avoid the issue we are discussing (I later fixed that bug in that week window). So anyone who ran FSO in that week window had this happen:
1) Game runs and sees there are new controls and enables them even though they are set to disabled (bug, but again that was fixed).
2) Game checks for default control bindings, sees they were NONE and saves that to the player file (again this bug was also fixed).
3) Player uses the same pilot for BtA, and the game reads the player pilot file and sees that the controls are NONE.
Ultimately this is a case of slight instability using nightlies, if a player was always using stable builds then that would not have happened. I know lots of player (including myself) use nightlies only though, so it's just an extra step we as nightly players have to be aware of.
Nevertheless, a fail safe script that checks for controls (even ones the player cleared manually) is a good idea. I unfortunately won't have time to develop it now, but once I am done with my thesis in 1.5 months I'll have time to get back to FSO SCP and script development.
EDIT: cycle presets cycles through whatever is in the mods control table, so use at your own risk. If the mod has only one control default specified then cycling will ontly change that one control.