Sorry if I’m misunderstanding, but from what you’ve just described, if the penalty is about realism, then shouldn’t a longer barrel length equate to a damage BONUS rather than a penalty?
EDIT: Ah, I missed the part where the .50’s BASE barrel length seems to be based on the M2, so the Barret’s barrel is actually shorter than the base, despite having a fairly long barrel by most rifle’s standards.
That said, the Barret really, really ought to have more damage. It’s total damage with a .50 BMG Ball round is 61, just barely edging out the Heavy Crossbow by one point. In comparison, the M2010 with a .300 Winchester Magnum does 70. The Barret has a higher piercing stat, but still.
You can’t tell me that a rifle using the round on the far left should do less base damage than one using the round adjacent to it.

Hell, it’s even out-damaged by the M1903 Springfield using .270 Winchester! Let’s just do a comparison on those rounds, using the mid-range size listed on wikipedia for each round:
.270:
140 gr (9 g) SP 2,916 ft/s (889 m/s) 2,644 ft⋅lbf (3,585 J)
.300:
190 gr (12.3 g) BTSP 3,083 ft/s (940 m/s) 4,027 ft⋅lbf (5,460 J)
.50 BMG:
700 gr (45 g) Barnes 2,978 ft/s (908 m/s) 13,971 ft⋅lbf (18,942 J)
And somehow, the rifle using the bottom round does less damage than one using the other two.