Sorry if this is too obvious and if you have already tried it but what about putting it in a separate folder called “the beatles (stereo)” or something like that? Looks like the hires version works as it is in a different folder.
With respect, I don’t think the latter problem is the same. As far as I am aware, the duplicates which are automatically played and included in total time are correctly displayed as duplicates in the pop-up shown above.
I think the OP’s problem can be solved with either new better folder structure, or better file tags, or both (belt and braces!).
Roon ID probably does not distinguish between mono and stereo. So, when it views disc 1 and 2 it sees the same album but duplicated.
The logic that provides auto ID in the vast majority of scenarios likely fails with this specific case. Although, on seconds thoughts, you have an album with two discs that totals 60 tracks. Roon is probably working correctly. You folder and tags say that you have a 60 track album if I follow what you have shown above.
I would change the disc number appendage to be [mono] and [stereo]