Im not putting words into your mouth, Bouncy. I'm merely implying that after 20 years of DOOM, it would be hard pressed to expect it to be perfectley intact as far as IWAD's go to during all the different releases and compilations. Some still contain the original IWAD's, but usually its PC-related releases (DOOM collection, STEAM via DosBOX instlaller, id anthology, etc).
There were even legality issues for them to try Vanilla DOOM through STEAM... id was sued for using DosBOX in a retail sale for trying to keep it as Vanilla as possible. They ended up having to pay royalties to the owner. I think that was a honest effort to deliver completely untainted, unmodded, straight up classic DOOM. They contained IWADs direct from v1.9 DOOM completely unaltered. You can't say they havent honored your vanilla requests in recent times, and they certainly have tried and done so... its STILL for sale if you want it.
The DOOM 3 BFG edition, on the other hand, was just a celebration release for 20 years, one giant bundle, cross platform, with as many non-legal issues addressed as possible. They want a quick and easy way to play through DOOM 1 and 2 in a near complete, yet "lite" option for those who wanted to give it another glance before or after playing the main event which is Doom 3. The release was likely intended to just be a on-the-fly index of DOOM anthology itself, never meant to be modded or extracted to be played as part of source ports, etc.
Now, name me one other series compilation of 20 years that came out COMPLETELY unaltered that is perfectley intact or not edited in some way, shape or form. Just the publisher changes and developer changes over those 20 years could even cause legalities that could mean alterations of contents alone.