There's not a button to remove the extra stuff right now, but you can open the bone in a hex editor, find it in the MDL0 file, and hex the part2offset to be 0. Then all you need to do is open the mdl0 in Brawlbox, change something, and then save and the bone will be 208 bytes in length.
The part2offset is at offset 0x6C (with the base being the start of the bone) and is a 4 byte long integer. Just change those 4 bytes to all 0s.
Edit:
I seem to have finished REFT parsing faster than I expected, thanks to a combination of Kryal's REFF structs and texture decoding functions, and Tcll's reft image header notes.