Because it was tuned like that. As above, the tuner probably wouldn't know about the leaks, they just tune with what they have and make suggestions later.
I just reviewed my last boost graph from Trent, 20 psi by 3700, 30 psi by 3900 on a .82 GTX3076, just to give you some idea. There isn't much difference between the .82 and .63 spool I believe, perhaps 200-300 revs, but the top end would feel so much better with the larger housing, and feel more responsive once on boost. As said, sort you issues first though.