If I was making a Dark Avengers theme team using both Norman Osborn and Bullseye... can I thunderbolt them while I use the Dark Avengers AtA for everyone else? And would it still be a theme?

Only 1 ATA per force, so you have to choose between them.

This is one of the reasons why I'm sort of 'meh' about the Dark Avengers ATA. If it's a strictly DA team I'm running, then the presence of the ATA will be helpful. If there are a lot of DA/T-bolts...then I'm probably going to run T-bolts (even though it's more expensive).

A force cannot consist of both the Thunderbolts ATA and the Dark Avengers ATA. A force may only have one ATA.

From p. 17 of the 2010 Core Rulebook:

Also note that, when playing an ATA, you must pay for every character with the linking keyword