Is my new amp TOO GOOD?

I have the Mc462 and a c53 and they are not super bright or etched or whatever you're hearing there. They're actually really neutral. Your room is probably bright or the speakers themselves. Running your set up with treble at -4 indicated there's an issue imo. You can download a free app like RTA analyzer and set your tone controls to neautral and play a few songs and you can see in real time if the treble in the room is tipped up or not and at what frequencies. If you use Roon you can then adjust it very finitely to trim down whichever frequencies are unusually bright. 

I fall into the break in crowd. I bought a very nice (to me) new solid state amp, and it took a well over 100 hours to break in. I pretty much just let the streamer play for days on end. Your tube gear probably needs more than that.

It really didn’t sound good at all straight out of the box. Give it time and don’t fuss with anything else like placement for a while.

My gosh this was a substantial upgrade. Integrated probably blended all your frequencies together versus separates that are substantially better.

My guess is it’s bringing out the speakers you have maybe in a different way. Maybe better maybe worse but your hearing them differently.

And the subwoofers probably need a lot of tuning because if they’re off probably the trebles gonna be impacted. I have gain settings on my amplifiers and when I adjusted them it reduced the trouble sound from the speakers. But I would avoid adjusting your treble so aggressively because you’ve really reduced it and I would focus on other areas.

Basically you’re hearing your speakers differently because the components you have are outstanding. I’m not a big fan of bell tweeters because they are very revealing and kind of annoying. I don’t even like the diamond tweeters I use on my Bowers speakers. So I’m thinking about sonus faber. Sometimes revealing may not be such a good idea for comfortable listening. 

Try different music because now you’re hearing the recording quality a lot better and because of this I am now very disturbed by the poor quality of most of the things I’m hearing because the engineers didn’t do a very good job sadly but I live with it but it does make even a bad recording sound better it’s just I’m noticing them more. Which is why revealing speakers can have their problems.

Final point, 90 dB is very very loud and approaches a danger zone and I'm not sure how big your room is. I would lower the volume and get used to lower volumes for your hearing health. You should be able to handle less volume now that you have a more revealing system.

May I ask the question: Are you using any silver interconnect cables? Silver can add a brightness to the presentation from my experience.

What jumped out as a red flag for me is the speaker positioning. 
11 feet apart is a bit much. What happens when your speakers are spread so far apart is you don’t get the midbass and midrange filled in. I have experienced the exact issue you’re describing and in my system I solved it permanently by moving the speakers closer together. My recommendation would be to start at about 7 feet measured between center of woofers. Toe in so that they cross about a foot behind your head. Listen to it and start moving them apart keeping the same toe in. I’m pretty certain that with speakers set between 7-8 feet apart you will eliminate this problem. Set your listening position to be approximately 84% of the distance between speakers (woofers).