I always read "Retrofitting OEM complete gear sets in an alternate transmission case is permitted (9.1.4.3.E.3)" as all of the gears from one box into another, presumably for fitment purposes. mix n match opens bigger doors. good / bad is debatable.

that said -
if anyone is considering a D series, go out and dig up HF or 4spds boxes and those from ZCs because they combine with Si boxes to have the gears you'll want for a close ratio 5spd.

Toyota C boxes will be fun... something like 28 years and MANY models running this family, with a lot of part interchangeability.

I'm betting there are more than a few VW combos available, too.

I'm with adam... shouldn't have read.