Editing hidden metadata in MP4?

Question

I've been trying to organize my music collection as of late, and this task includes cleaning up the metadata for more effecient viewing on my iPod.  I've come across a bit of a quandary, though, specifically regarding MP4s purchased directly through iTunes.  It seems to me that there must be hidden metadata associated with these files (searches both here and on Google seem to back this theory up, as well) ... metadata that is not editable by either iTunes itself, nor the third-party program "mp3Tag." 
It is proving quite problematic to my organization as a whole.  Specifically, I have been removing album info from most of my collection, and these hidden tags seem to override what I have designated not only for the song in question, but every other song with removed album info when viewed on the iPod.
I have found that I can circumvent this problem by having iTunes create an MP3 version of the song, then deleting the purchased version; however, I am mildly concerned with loss of quality in converting from lossy to lossy in this way.
So... the question.  Is there any way to actually edit these apparently hidden metadata values?  My research into the subject has only found 8-year-old posts that direct me to long discontinued, no longer available software.  If not, is there any way I might convert to MP3 without quality loss?  As I understand it, you can't get lossless formats through iTunes via download.

Answer 1

Fortunatly, I was wise enough to make a backup of my collection before starting in on this process, so hopefully any regrets had will be limited at worst.
The tags in question, though, don't appear to be editable by any program I've yet run across, though they (the tags) clearly exist. 
Below is an example of these as viewed in Notepad++, on a song that I (for the purposes of this test) stripped all metadata from in both iTunes and MP3tag.
H QR¤ Q›  Qâë R+€ RtN R¸æ S   SHå S“® SÜ  T$d TnV Tµæ Tû# UCÙ U‰F UÌG V — VN§ VŽ³ VÑù W 5 WOï Wæ WÐÞ X À XS‚ X•· Xפ Y w YYp Y›Ê YÞ$ Z Ü ZV_ Z™  Zפ [ & [Zs [›  [Ù  \ h \X€ \œX \Û½ ]   ]\ß ]œÿ ]ßõ ^!ê ^d2 ^¦ð ^ç] _)Ì _hƒ _©Ý _í7 `*l `kT `¬- `ðN a1É avX a¸— aõè b2{ bla b¥’ bÝ£ c M cO” c‰B cÂÀ cü6 d5u do4 d¬Y dé   pÖudta  pÎmeta       "hdlr        mdirappl            h7ilst   ¼----    mean    com.apple.iTunes    name    iTunSMPB   „data         00000000 00000840 000000AC 0000000000781314 00000000 00000000 00000000 00000000 00000000 00000000 00000000 00000000   ¢----    mean    com.apple.iTunes    name    iTunNORM   jdata         00000C9A 00000D95 00004CA3 00004A8E 00023BCB 00023BCB 000079B2 000079B2 00001738 00001738    ©nam    data        Sabotage   $©ART    data        Beastie Boys   $aART    data        Beastie Boys    cpil    data             pgap    data            ,©day   $data        1994-06-04T07:00:00Z   )apID   !data        **MY iTUNES ACCOUNT**   Mcprt   Edata        â„—  1994 Capitol Records, Inc.. All rights reserved.    cnID    data        +3$“    rtng    data             atID    data           —    plID    data            +3!û    geID    data           x    sfID    data          0Q    stik    data            +purd   #data        2014-01-28 02:01:55   3xid    +data        umgglobal:isrc:USCA29400020   ----    mean    com.apple.iTunes    name    iTunMOVI   Udata        <?xml version="1.0" encoding="UTF-8"?>
I hadn't considered giving them a common album title, rather than just removing it outright. 
*tests that*
While it does what I need it to do on the iPod, unfortunately, it would completely wreck usability on iTunes itself.  Back to the drawing board.
A quick recap of my options...
- Accept the fact that I wont be able to change these tags, and have a slightly more "littered" album cover view on the iPod.
- Restore my backups and go back to a purely playlist form of organization.
- Convert all iTunes-purchased songs from M4A to MP3 to "scrub" the hidden tags, and suffer potential quality loss.
Looks to me like the only sensible answer is to go back to playlists.