When you're playing restricted Marvel, does that mean you can't T'bolt to DC TAs? Same question with reverse.

Nope. You can T'Bolt any TA from any Universe.

There is one limitation. As of Danger Room, Morlocks and Serpent Society are considered to be Retired. So, if Retirement is in effect, you cannot T'Bolt these Team Affiliations. When, or if, these TA's will become legal again is unknown.

Actually, Serpent Society is not retired yet - Asp is available in Fantastic Forces. Right now, Skrulls, Crusade, 2000AD, and the aforementioned Morloks are the only retired team abilities (all of the other Indy team abilities are retired as well except Arachnos and Freedom Phalanx, but there are non-Indy alternatives to all of them except those listed above).

Skrulls will apparently be coming back with Super Nova and Serpent Society will retire when FF retires, unless another SS member gets made (indications from Seth are that there wil not be).

I beg to differ. The Marvel Heroclix Errata and Clarifications document states the following in its Thunderbolts entry (page 7):
The way I read this is that if the tournament is Marvel Only, then only Marvel TAs may be copied. If you are playing DC Only, you cannot use Thunderbolts at all.

By the way, Serpent Society is NOT retired. The last member of that team to come out was REV Asp in Fantastic Forces, which has not yet been retired. As of now, Morlocks, Skrulls and all the Indy TAs are retired (although most Indy TAs have equivalents in other universes...).

My apologies. I guess I didn't know the answer after all . Thanks for the corrections.

Thanks for the answers!

I'd say that at that point, since you're dealing with a scenario, it would be a question for the judge running the event.