So I found something on GTA that may or may not be a direct reference to Thomas the Tank Engine. In one of the rail yards, you can find a pair of what appear to be troublesome trucks. I'll let you decide for yourself.

GTA?

6006526
Grand Theft Auto. Number five, to be precise.

6006522 Kind of looks like them, but then again it kind of doesn't.

6006572
Given this game's blatant ripoff of Knight Rider, Halo, Fast and Furious, and even Mythbusters, Rockstar probably only changed just enough to slip through the copyright net, but still be recognizable.

6006522
Those are pretty common truck, even today on Heritage Railways, so I don't think it's a direct reference.

6006649
Maybe not, but it's a nice thought.

6006522
I agree it is a possible easter egg but in all honesty, it proabably isn't. On that note:

The Engines always think they are so clever