I don't know that they physically made the trans thicker? I have heard a few times that the later boxes were stronger, but no specified reason for it. I know that the early boxes (pre V5/6 I think it was) had less attachment points to the engine, so that was supposed to help make them stronger, I imagine it could potentially allow them to locate more rigidly to the box, reducing flex etc?
However realistically, as long as you don't want to launch constantly, the box if it has been treated with respect should not differ majorly between anything >2000. Same goes for flat shifting, just say no.
If you were looking at a V1/2 WRX or a BC/F5 Legacy I would say yes the boxes are weaker as I have seen the results of launching killing them. But most of them don't have original boxes now anymore due to them being broken...