Sorry but in my experience every single tc3 chassis is tweaked, no matter the generation. The motor corner is lifted up. You probably tried this with a naked chassis. Of course the chassis itself in decently close to dead flat on a glass plate, if you have removed the injection blurr below.
Now install the cam+ clamp, and even with the slightest tightening, just enough to prevent the cam from moving, your chassis is tweaked. With the car put on 4 scales, try to do this and the weight changes are just scary.
Sooo, to answer your trivia... I'd say
1) droop tabs
2) the "wall" around the motor was half the height of the chassis on the first versions. Later it was the whole height of the chassis.
3) Ugly plastic scar on the plastic between every battery slots, on late versions.
4) perhaps a little molded "shim" on one or both sides of the motor mount, where the clamp comes? not sur about this one.
the inner reinforcements ( "walls" ) have also varied along the years...
It'd be funny to compare the first prod Tc3 with their latest batch. Not that many parts would be identical...