Actually found a provisional workaround for this. Export to GIF instead of PNG tilemap. Then crop the GIF in the tool of your choice, to fox ex. 16 x 16, then manually copy each GIF frame to a new PNG tilemap (for ex. 64 x 64). Of course, depending on the animation length this can be nuts, but for small bursts and short animations it is laborious but it works fine.
I have a better workaround: Export to gif then crop, like you said, but then use a Gimp script to make a spritesheet from the layers.
Ex.:
registry.gimp.org/node/20943