Lore has nothing to do with the recycling of iconic creatures and other elements. This practice can even make the universe much more shallow and is generally not advisable from a lore pov (much less from a creative one - the more elements you recycle, the less cohesive the world, since the designers aren't creatively challenged anymore).

We knew nothing about the Commonwealth wildlife and it could habe been something completely different.

Unfortunately Bethesda decided to have the same things everywhere in the Fallout world. Don't expect any non-DLC Fallout to ever miss the Brotherhood or Deathclaws or Radscorpions.

It's the freaking giant mole rats that get me. Why the heck are they everywhere. In the east shouldn't we have had giant squirrel rats instead?

And where the heck were all the snakes in NV anyway? I grew up in that part of the country and we had plenty of snakes ... no mole rats though.