Don't worry, I have both cartridges and am certain that I can pee further.
You are correct in case capacity difference. I find that to be an advantage and a also on that note you, have 7 grains more in the smaller case's projectile. I will observe that you are not commenting from a point of strength in using the same powder for both cartridges in your drag race. CFE BLK despite it's name does a lot better in the x39 than the BLK for 125's. It is my belief that it was envisioned for the subsonic loads and fouling in suppressors rather than pushing 125's around as it requires 12 grains to make 1060fps instead of 8.
You're using .7 grains over compressed in Hogdgons online data for the BLK and getting 100 fps better than what it advertises. For the x39 you're right on the book data. I'm thinking that if you took a 125 and Lil Gun or just Lil Gun and the 130 you'd narrow the gap a bit.