ehe...I knew that somebody will ask this...
well...yes, you can enable it too if you like....a new scan will then list a lot of unneeded files for you. The reason why it's not enabled by default is that the rom merge information was too often too wrong in MAME's past. (However cmpro tried to fix this automatically).
The whole story is about differently named files within a parent clone relationship which are physically identical. Usually there is a reason for the diffent name (to match the real IC name on the boards), so for cmpro it means: different names = different roms...your somehow turn this off when enabling rom merge tag parsing. If you currently have a differently named but identical rom in a clone, it will be removed if you got a copy of it already in the parent (with a different name).
In times of multi-terabyte hds and maniacs who collect a full mame set, noone should really care about the saved disk space when enabling it...but anyway...it's your personal taste...
actually when I do some brainstorming about a rewrite of cmpro I think of removing all special rules.....it will end in something like:
- only xml datfiles (MAME dtd)
- other (xml) formats need to do a xslt transformation
- trust in the given xml, i.e. always use merge tags, don't care possible issues during fullmerging based on different roms with identical names (the scanner/rebuilder should handle that) etc..etc...
- no more support for old style rules (like old bad_dump handling via ~crc32)
etc etc...should make life much more easy...at least for the developer

...but hey...not a single line is written yet....