It sounds like you'll need to submit a feature request to the PT team. You can do that via the Help > Give Feedback dialogue.
My guess is that they simply didn't imagine that people would use so many different icons, and so didn't consider your situation (I've only ever seen one project use that many before, and in actual practice they weren't really _using_ most of them).
I would guess that allowing the same icons to be used multiple times in different colors would be a very simple fix on their part, though that doesn't mean they would have the time to do it (they have very few developers doing the actual work). On the other hand, adding new icons (meaning designing new icons) is less likely a "simple" fix.