I think there's 2 schools of thought with the bell housing/bearing retainer issue. T5 bearing retainers are relatively abundant and easy to get, so machining those to fit is probably the easier of the 2 choices. There's a second reason for that, too; they're easy to chuck up in a lathe and buzz a few thousandths off of the outer diameter. On the other hand, how many people will step up and restore a MII? If you're never going to be concerned with restoring it to original, setting up and boring the retainer hole on the bell housing makes it easier to swap transmissions and/or bearing retainers if the situation ever arises, making repair and maintenance a lot easier. All of that being said, the bell housings aren't being made anymore and there are a limited number of them. So, if it's ever needed to be used with the old RAD transmission it will be useless UNLESS someone does some work to the mating pieces again. I can only see that being a purist, though - and really, how many of those types are there out there?
I think it boils down to being a personal preference. If I had to do it all over again, I think I'd have set up my bell housing and made it work that way.