It seems all the GIF encoders out there just take the easiest way out. GIF itself (from what little studying I've done of the spec) isn't such a terrible "codec" to work with, and it has features comparable to basic, decent video codecs. It has the potential to be decent (color space issues aside). The problem is with the crappy-ass encoders that take the laziest approach possible, rendering each frame separately, literally not cross-optimizing anything, applying random dithering in hopes it'll look OK on the pathetic monitors that were the best the 80s had to offer, and trying to do it all with as little RAM and CPU time as possible with no regard for searching for similarities across frames and finding ways to optimize the results appropriately.
There's no reason a good GIF encoder couldn't do what you did in your post. I don't know if one actually exists - I gave up on GIF long ago, after a string of horrendous failures similar to yours, where even the simplest animations would result in 1 MiB outputs and have horrible dithering banding throughout.
Add to that the similar disregard in decoding in browsers - where a 256 KiB GIF takes a full 45 seconds to load (stuttering and freezing for 20 seconds at a time) on a 50mpbs connection running on an i7 CPU as a result of the combined failure of encoders and decoders alike. It's pathetic.
APNG is at least a chance to wipe the slate clean.
Anyway, nifty animator there. Thanks for sharing, it'll really come in handy for screencast demos.