LOL - I will be the last guy chewing them out....I don't pretend to understand why things like this happen....not being an insider and all.
For "Brain Salad Surgery", it probably went down like this:
Band approves Jakko's new stereo mix (which overall is very good), doesn't approve the 5.1 mix, then suddenly somebody discovers the "Karn Evil 9 3rd Impression" Bass Solo and says "Whoa! We can't have this going out to the mass public like it is! So why don't we stick the 5.1 mix just in the Super Deluxe Edition, that way we make sure that those who really want it have to pay extra for it?"
Therefore they solved one problem by creating another one…still, they tarnished their reputation so badly IMO, and they know it too.
We'll see where things go from here...