I'm using a Hotheads adapter for my 331 hemi to Chevy manual transmission. I put the adapter on the block and the bell housing to that. Everything fits fine, but the flywheel and clutch are exposed to the elments of the road and weather. The Chevy bell housing had a tin plate to cover the flywheel but there is no room for that plate between adapter and bell housing. I'm sure I could make something to fit. Surprised that there wasn't one from Hotheads. Anyone dealt with this before?
Which 331? Extended bell or standard? (I'm assuming standard late 331 block) Did you call Hot Heads and ask them about it? My experience with Hot Heads and their adapters is that they don't always know just EXACTLY all the details of their adapter setups. I'm not sure I'm 100% understanding your issue (a picture would help), but you may have to choose a different bell housing. I ended up having to switch to a Lakewood style stamped steel bell housing to eliminate a starter problem I was having... which of course was not supposed to be a problem with that adapter.
Some adapters like my early hemi to Mopar transmission adapter are made so that the original starter shields and lower dust shields can be used. Some others are not made that way.
I have a vintage Speed Gems adapter for a SBC to 39 Ford trans that is the same way, you can see almost half the backside of the flywheel. I think I'm just going to make a sheet metal plate to cover it.