First of all, there is no need to generate a datfile. Profiler->create let's you import the data from the MAME binary directly which is the prefered method. At the end of the import cmpro asks you if you want to import software lists, too. (Dullaron...In that dialog is the warning you want to see).
Autoassign sysdefpaths tries to match your setup rompaths against the imported data and based on a highest-sum-per-softwarelists it decides which rompath belongs to which software lists. If you don't have any sets it will of course assign everything to your 1st rompath.
Why it simply doesn't scan childs, well, because there is an offical way how sets are stored. rompath\setname\file 1..file n for decompressed sets or rompath\setname.zip (.rar/.7z) for compressed sets. Even sets with subfolders are supported, so of course you can't simply put everything into one big folder with subfolders. You need to make yourself some thoughts about rompaths are organized.
But anyway, software lists are supported as single profiles anyway and combined with the batcher you can scan them in a queue. Simply use the xml files from MAME's hash folder within the profiler. The all-in-one-softwarelists-and-mame/mess is just one alternative.
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