I personally handle transition tracks in 2 different ways:
#1 for the ones that I don't care about FX being quantized and are simple BPM transitions I just manually type the starting BPM and ending BPM in the tag somewhere.
#2 for the ones that I really really need the beat grid to be perfect - I analyze them in dynamic mode plus I take the time with Rekordbox and manually push and pull each beat marker into place.... It takes a while but its worth it in the end! I also really only have maybe 10 transition tracks, if you have a lot then I feel your pain. :)