It would be handy if there was an option for the ROM-Path setting to include all subfolders. I know for MAME and other arcade emulators this does not make any sense. For using other DAT files to scan a "GoodXXX" set it makes perfect sense. Especially if you rename your "Good" sets using the "dirs" option.
Romsubfolders aren't supported but in most cases you can simply use setsubfolder definitions in the datfile...like: rom ( test\bla.bin ... ). So simply reorganize the datfile.
Back in the time when I did some *GoodTools* datfiles, I also had several dats included per system. One which had them set by set and one which kept them in one folder.