You can get replacement "tube cans" from Mesa on their parts web site. If it is new, send them an email with some photos and they should send you replacement cans with o-rings (probably cheaper as an assembly than messing with just the o-rings) for free. At least, i would hope they would. I bought a couple replacements on top of a tube order and they are dirt cheap (you'll pay more for shipping if you get the tube cans alone).
Now, does it make a difference? I do not know. I do know that my Mark V had a "microphonic" sounding tube issue during a gig. Testing at home, I swapped the V1 tube the microphonics was gone, then I put the original V1 tube back in again (just to double check if it rang when I hit it with a pencil), and it did not ring. So, I put the can back on V1 and buttoned everything back up and the "microphonic" ringing returned, even at low volumes. I removed the tube can and noticed it did not have the o-ring, and the ringing disappeared! So, I took one from the V7 tube can and I have had not had a microphonic issue since. Then I ordered some cans with o-rings as back-up.
I spoke with a Mesa tech (Kris) about this on the phone and he claimed that the o-ring should not have a difference. He might be right, and my experience may just have been a coincidence (although, I cannot explain how the 'microphonic' tube healed itself), but nonetheless, the cans/o-rings are dirt cheap, so why not have a couple spares and make sure the can does not come into hard contact with the mounting board?
Mace