The theory being that the higher BB on the track bike will move the TT higher off the ground and therefore for clearance sake it is best to size the track bike smaller.

I personally don't buy into this. I size my frames based on when I'm on the bike, not when I'm standing over the TT.

For me it means the TT of my track bike is touching my pubic bone when I'm standing over it. So what. Once I'm on the bike, I have no issues. And the bike fits right.