Yes, but not enough that they’re really incompatible.
IIRC if you use new callipers with older levers (pre 2007 ish) you end up with more leverage (i.e. the lever moves a bit more but you also have more power but the pads sit closer to the rim), using new levers with old callipers had the opposite effect, the brakes felt a bit wooden as the lever doesn’t move as much.
But none of the aftermarket brake people have changed AFAIK which shows how little effect it really had (there aren’t two variations of BB7’s, Spyres, HY-RD, V-Twin, Juin Tech etc).
It’s not like V’s versus road pull which is almost double.
If you’ve got a marked difference then I’d look at the cables and pads.