Well, after quasi-successful attempts to use the id3lib that comes with older version of emptool, I realized that my mistake was starting off with an unclean id3lib directory. I had done a "make clean" but there's apparently a "make distclean" which cleans up other stuff. After doing that, I was able to cross-compile it.

I guess I was just thrown off by the fact that configure was telling me "Don't cross-compile." I guess I'll just be more brave next time.