FQM indirectly lists the modified files.
FQM Deluxe has a modded pop bonus curve to better reflect the drastically increased levels of population on planets (raised levels for most bonuses). For use with P&N, I suggest you just use the P&N settings file, and change the max systems to 255 (the FQM setting), or whatever you want (no more than 255 of course).
You might want to consider bringing the population levels of the planets back down to normal SE4 levels though, unless you don't mind HWs getting 200% the bonus they normally would.
If you make a map with FQM Standard and use it in another mod, all stellar objects will retain the abilities that they were given when the map was generated. StellarAbilities.txt (and a bunch of others, all the modded ones in FQM Standard) is only accessed when the map is created, and then never again.
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It *is* possible to carry over everything special, such as the gazillions of storms AND THEIR EFFECTS, right?
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You can not use a map generated with FQM Deluxe in any other mod (unless ofc it has had FQM Deluxe mixed with it). Only FQM Standard maps can be used in other mods (or normal game). They are much less interesting though. 
[ May 26, 2003, 10:41: Message edited by: Imperator Fyron ]