Basically the FMC uses:
It actually doesn’t care about the runway length, obstacles, climb limits, brake energy. These are accounted for in the specific runway takeoff weight calculation.
The problem with using the FMS speeds that are 2-3 kts different from charted value will only become apparent when it is too late~! Imagine yourself in the court of inquiry trying to explain why you spent 5 minutes at pushback calculating the limiting weight and speeds from charted values AND THEN ignored them!
I would strongly suggest that if there is a difference, that you overwrite the FMS speeds.
Mutt