For an individual song, yes, but I don't see how to do that for several thousand.

(Assuming latest version)...

Uncheck "Custom file selection mode". Check "Include Subirs" (under the Execute button). It will do every single MP3 file in the directory tree below the specified working directory.

The tab labeled "Auto tag (from filenames)" only seems to write to v1

(Assuming latest version)...

File/Settings: Primary ID3 version= V2, Uncheck perform write operations on both tag versions when possible.