I'll update the OP with this, and granted this formula only applies to Supergirl as far as I know. And again, this is level handicap as well as competitive mode on.
When using Supergirl, Supergirl herself and Superman have 1100 HP to bring down. Atrocitus and Batman have ~1250 HP (technically it's 1249.81, for whatever reason it being such a number -__-, but it is what it is). To find the percentage, just divide the decimal numbers by the correlating HP, multiply by 10, and there you go. They all come out to nearly the exact same, with tenths of damage (0.1% - 0.8%) being the only difference.
So using the combo damage in the OP:
The damage for the Kyrptonians is 298.91
( 298.91 / 1100 ) x 10 = 27% (27.17)
The damage for Atrocitus and Batman is 332.13
( 332.13 / 1250 ) x 10 = 26.5% (26.57)
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One of the larger bnb's she has:
On Atrocitus/Batman, is 413.91
( 413.91 / 1250) x 10 = 33% (33.11)
On the Kryptonians, is 372.52
(372.52 / 1100) x 10 = 34% (33.86)
The change in numbers don't seem to exceed 1%....I just find it kinda nonsensical to have such dramatic numbers when it ultimately doesn't even exceed a 1% difference when put into percentage. But maybe that's just me