I guess you've already got your chain set up, though my first thought in your situation would be to consider storing any meta data you need in a separate file with the same name but different extension.
I've thought about adding a meta data section to the format itself before. Part of the problem is backwards compatibility--suddenly every single library out there is broken :/. It would've been nice to have this from the beginning, but it was just a tool for myself that I never expected would start getting rather big and have all these other users and libraries come along
A couple times I've wanted to add things to the format, but in the end always decide that I like it as simple as possible, and could/would use separate files to solve any other needs.
Anyway, it's now on the list of features to consider.
One approach to preserve compatibility: What if the config file could be used to specify a separate format, and all your files would be manipulated in that alternate format instead. That could accommodate any additional format requests, like meta data, without complexifying the main format. It adds a little complexity on the REXPaint side, but maybe it's doable without too much of a headache...