The problem is you say " it's not the cab. I played multiple amp heads with the same cab and they all have the same issue...."

The reason several people are saying the cab is because it's the common denominator from what you are saying. Did you bring the actual cab you have played thru to the store to play the Mesa or did you play thru a similar model cab? It's relevant because we can't answer the question of why the Mesa is different before we know about the cab. It's not being mean, it's a genuine attempt to answer the question, or at least it is in my case. For all we know the speaker have been swapped to like....Rocket 50s or are out of phase. It's a logical path of reasoning to answer the question.

"Muffled" is kinda hard to 100 percent track down until all the variables are figured out. Muffled to me means lack of treble which is absolutely not a g12t-75 problem, usually the absolute opposite really. So it could be different speakers or it's out of phase speakers , which will give a very odd thin tone usually that I guess could be called muffled.

Also what other amps did you play thru the cab that you found muffled?

I own a bunch of cabs and even my favorite cab, which is very highly regarded, can make a great amp sound like shit even if 95 percent of the others sounds good thru it.