1a) "Log"
When running the commandline version, the log is the printed output with various warn levels (info/warn/error). You can redirect it into a file if you want. When running the UI version, the log area is at the bottom of each screen. It's resizeable, scrollable and you can even copy all entries to the clipboard. If it's "2 lines", then you should adjust it.
1b) "backup path"
Well, due to the fact that rompaths are reserved for your roms, it's pretty obvious that the backup path can't be a subpath of any rompath, otherwise the scanner would detect it as unneeded. That's why the log informs you.
2) Softwarelist: First of all the question would be are you talking about a -listsoftware import from a MAME binary or a single load of a software list (hash file folder). I expect you do a -listsoftware import from a mame binary and then the following happens: clrmame rememebers a hash for the binary and a hash of its hash folder where the software list xmls are stored to see if it needs to reget the data and doesn't use the cache. So it does see if files do change inside the hashfolder or the mame binary itself changes. In this case, it reimports the data. Now you might do your changes in a different folder, then there is a settings in settings.xml "Settings/HashFolder" where you can specify your path and then this is monitored for changes.
3) Scan versus New Scan
This has nothing to do with cached XML data. A "New Scan" ignores possible existing previous results and rescans all machines while a "Scan" only rechecks the machines which had issues in a previous Scan or New Scan. The result is remembered and store. If there is no existing result, a "scan" will do a "new scan"
So....to sum it up: no bugs