I've just had an "I've been a fracking idiot" moment, and there's now a solution that will solve my IBP problem (also the Freaking Intimidating Ogre problem for firearms).
Alter the prerequisites line to read "<ability> of 13+, plus any racial or racial template modifiers the character has to <ability>". That way the IBP, who gets minimum a -4 to Strength needs only have a 9+ Strength to shift melee attacks to, say, Dexterity, while the FIO who gets minimum +4 would need a 17+. Thus, every race has the same requirement in terms of how much investment they need in the trait. While I'll grant that this still gives considerable bonuses (IBP getting a +4 to Dex means you're working on something like a +5 bonus to melee combat if they're not optimized to that), it also means that IBPs and FIOs won't be defenseless in one form of combat or another (the FIO in a firefight is a very extreme example, since low Dex screws her twice, not to mention the Size modifiers and the difficulty finding any reasonable form of cover).
I realize I may be a niche market with my postulating IBP/FIO type characters in games, but I also know my player's tastes and have to react to them.
EDIT - to clarify an example and to remove references to comboats.
Just goes to show, don't work for the Navy.