I'm sure that order.j2b always starts from the beginning, so JJ2 definitely does not using hardcoded restart positions for that track, and I doubt it would for any other track. The track, however, does replay nearly all of the same patterns before starting from the beginning again.

From what I can tell, xm files created with different restart positions create different j2b files through MOD2J2B so there is a chance that the relevant data is stored in the j2b file. JJ2's Galaxy Music System doesn't appear to support restart positions whether for mod tracks or j2b files, so you wouldn't be able to find out through JJ2 if j2b files store restart positions.