A.
No. The first item that says "Fix via Override" requires you to hit "Override" to delete the already existing file, and replace it with the new one that you are currently processing with FileBot. If you do not hit "Override" then this file will not be processed. If you hit "Override" then the already existing file will be deleted, and this type of conflict will disappear from the list of conflicts.
B.
Yes. The set of files that you are currently processing with FileBot has multiple files that map to the same destination path via your custom format, and thus FileBot has chosen to only process the higher quality file. One of the files will be processed. The others won't get processed. Hitting "Override" has no effect on this kind of conflict.
EDIT:
FileBot r9084 and higher will improve conflict descriptions and button labels:
