I think that it is a just case of a flat master vs one tweaked with a bit of equalisation. As with the 7" Sony Japan re-releases vs AF both versions have gained praise as well as have their detractors, some complaints are about the use of smiley face equalisation.In my opinion, the quad mix of The Best of The Doors that appears on the Rhino Blu-Ray is the best-sounding digital quad reissue to come out of Warners, and no surprise because it was remastered by Bruce Botnick himself.
For me it even bests Steve Hoffman's remaster of the same album for the AF SACD - even though the AF SACD is from the original master and the Rhino is from an LP copy tape, Hoffman's mastering sounds floppy and lifeless by comparison to Botnick's work.
I have always used a bit of smiley face (bass and treble boost) with vintage recordings. So whether such equalisation is applied already or not it can be corrected simply (adjusted to your individual taste) with the twist of a couple of knobs on vintage systems at least.