The images were purposely not cropped because aligning different sized images to have the exact same origin would be incredibly difficult and nearly impossible to maintain (in case you change any image). Even cropped versions would still be incredibly wasteful.
Took me a bit to get the hang of too.
Arimas methods are spot on.
My method:
I export sprite sheets from utility, in a row per angle. (8 isometric angles)
Import sprite sheet(s).
Resize entire animation (per angle/row) so resulting image in the center is the size I want, then crop entire animation by holding shift while cropping.
I refrain from changing origin point 0, so the frames always align neatly the same.
The only downside I really noticed, is having lots of animations (with all angles) has the potential to enormously bloat the program.
Not so much due to inefficient sheet creation, but the sheer amount of images involved.