The answer is no, depending on what powders you use. If only Goex 3F and 2F, the 3f should give more velocity, regardless of barrel length. For part of a comparison in a 24" .58 Leman flintlock I built, see "Shooting Accessories" board, my post of 2/06/18, "Powder Tests in a .58 Leman flint elk rifle". And The Hunting Journal, "A Utah Pronghorn Hunt" where I tested some powders in a 32" .50 caliber rifle I built. Since my .58 Leman post, I have shot more powders but not posted about them yet. For each powder, I made a measure that holds exactly 100 grains. Here are the results to date, remember, exactly 100 grains of each powder:
Goex 3F 1486 fps
Goex 2F 1308 fps(seems too low, but all good patches)
Olde Eynsford 3F 1543 fps
Olde Eynsford 2F 1526 fps
Swiss 2F 1598 fps
Olde Eynsford 1 1/2F 1522 fps
Swiss 1 1/2F 1413 fps
Alliant Black MZ (90) with 10 gr Goex 2F 1622 fps
Triple 7 2F (90) with 10 gr Goex 2F 1648 fps.
Best groups for four shots at 50 yards were 1.6" for Swiss 2F, 1.7" for OE 1 1/2F, 1.8" for Goex 2F and 2.2" for OE 3F. The Goex 3F went 4.0"
I also shot six black powders in my .50 antelope rifle, 100 grains each, so have that comparison in a 32" barrel. Eleven shots of Goex 3F averaged 1794 fps and 6 shots of Goex 2F averaged 1792 fps. Sometimes you get velocity readings that you can't explain, but they are real.