The two biggest problems I see with this suggestion is that player decisions will have less of an effect, and it adds an inconsistent behaviour to weapons.
Clip size rounding is absolutely intentional in how the game is designed. To give an example of what I mean by player decisions having less effect: "Charged Rounds would give damage but also increase reload time, Burst Rounds can increase AoE and reduce reload. Both ammo choices are pretty good, so I'll just use whatever I like."
Instead, players are encouraged to reason: "Charged Rounds is stronger on weapons with low clip size because it doesn't suffer from ammo loss and lower rate of fire as much. Burst Rounds do better on fast firing weapons with higher clip size and AoE because et cetera, et cetera."
Certain ammo types work better with certain guns, certain guns work better on and against certain ships. A well designed game (like GOIO) would make players think about those elements, learn what works better, and consider all the information when making a decision.
Taking the difference in ammo gain/loss and applying it via a percentage-based modifier would really just affect weapons with low clip size (1-3). This gives an inconsistent behaviour for weapons in general and is needless complexity; exclusive rules should always be an element of the weapon itself.
@MagKel: You definitely saw it coming.
I can be pretty antagonistic to many ideas suggested; mainly because I've spent
a lot of time measuring and studying GOIO's game design in depth, while also rationalizing and playing competitively.