Well yes, you have to specify the prefered merge mode in scanner (rebuilder/merger)....if was still on split cmpro tries to generate sets in split mode.....and moans about every thing clone-like in a parent set.
"hash collision name" mode...well....as mentioned, when using full merged sets you can't simply put everything in one archive file since there are some sets which have identically named files with different content in a parent clone relationship. So merging them would overwrite one of the files. For such sets, cmpro automatically generates subfolders named after the clone.
Some users (and your collection provider seems to be one of them) prefers this full merging storing method (subfolders for clones within the parent) for each and any set...not only for the ones with such hash/name collisions. So by turning this option on, you will follow this method.
Torrent7z ...that's well...a different story. Fact is, t7z files are not fully compatible with the latest official 7z. For example 7z moans about extra data found at the end of the file (since t7z adds some stuff there) and I can't tell you which operations would fail when working on the files. Of course you can select a t7z binary in the compressor settings but keep in mind that a) I don't give any support on it and b) t7z compressing is most likely an overkill for scanning/fixing since the sets need to be reorganized over and over again. So a better way is most likely do a batch t7z recompress after scanning/fixing.
Little update to previous post: If you don't turn on the hash collision mode, cmpro will fix your files if the 7z settings are ok. This means if you have a solid 7z archive, your compression settings need to be adjusted, since the default ones will result in operating failures (like you cannot delete a file from a solid 7z file without turning on solid mode).
So to sum it up: Yes, cmpro will handle 7z/merged/t7z for your.....but the price for it (time you'd better spend somewhere else) is not really worth it.....For rare diskspace solid 7z fully merged sets might be fine (but not really in days of multi-terabyte hds)...but for fixing work it's a real pain in the a**. Solid archives or t7z...each operation will take long since the full archive needs updating/reorganizing..
Really...stick with zip and split sets ;-)