I can modify the IPB files, that's not a problem.
And whatever do you do when that is not the goal? when you actually need to modify default functionality in an application(not the skin)?
You mod your files too to save this(which, frankly.... I've not heard of, or seen, on forums with >20k online at once... I'm CERTAIN Ryan H and others would have been on this like white on rice as well)?
But it becomes a problem when I'd need to do the same file hacks after each upgrade (been there, done that), which is why an easy way to include a single php-include across all skins would be the ideal solution.