Haven't done too much with BKM yet, but this seems to
be a similar import/export problem to that documented
in bug #616623.
When I import in my Mozilla bookmarks file, the "tab
groups" that I have bookmarked get converted into
normal folders w/in BKM.
This same conversion gets carried over into the export
as well. I don't use Opera much, so have not yet
tested it there.
Hopefully, both of these bugs can be addressed. This
program looks like it could be quite promising.