Lara--We also use Handbrake to convert DVD Video to mp4. I hadn't noticed this before either, so I ran DROID and am experiencing the same behavior, with no format results for mp4s from Handbrake while mp4s from our digitization vendor display a PUID, MIME type, and format name.
Viewing the files in a hex editor, the Handbrake file signature doesn't match the mp4 format signature in PRONOM, which is likely why DROID won't recognize it as an mp4 file. I don't have the expertise to know whether there is an issue with file created by Handbrake or if the file is valid and the PRONOM signature needs expansion.
Created by Handbrake, not identified by DROID
00000020667479706D70343200000200 | ... ftypmp42....
69736F6D69736F32617663316D703431 | isomiso2avc1mp41
Created by digitization vendor, identified by DROID
00000018667479706D70343200000000 | ....ftypmp42....
6D7034326D703431001474616D6F6F76 | mp42mp41..tamoov
PUID: fmt/199
66747970{0-64} | {4}ftyp{0-64}
(6D703432|6D703431|69736F6D|69736F32)*6D6F6F76 | (mp42|mp41|isom|iso2)*moov
I've bolded where the signature matches PRONOM and bold underlined the part from the Handbrake conversion file that doesn't match.
Keith