Well, actually you can't do anything about the messages (besides hiding them via the hide option) unless you change the MAME source code.
- Alternative Samplefolder will be added as sample-only set
Well, there are sets in MAME which use an alternative sample folder which isn't listed at all in the MAME -listxml output. For correctness and easy scanning, this set will be added (containing only the sample definitions).
- Possible wrong nodump definition found
Well, here you got an effect where equally named roms within a parent/clone relationship are once listed as a nodump and the other time as a valid rom with a hash. You can decided if you want to keep the nodump or want to use the same hash for it.
- Can't merge set due to equal names for different ROM hashes
There are cases where equally named roms within a parent/clone relationship are not identical (different hashes). So if you try to full merge these sets without adding subfolders to the archive, you will overwrite one of them. So you can decide if you want to be forced to splitmerge mode or remove parent/clone relationship for the set in question.
Again, these are all events coming from the MAME database. You as an enduser can't do anything about it....as a MAME developer you got pros and cons for each root cause of these events....So...live with it