On both of my Bombardier machines, the nut goes on the outside. That's how they came to me, at least.
But this is borne out by the fact that the track guides have square holes, for fitting carriage bolt heads through, but the grousers do not. Additionally, you will find that trying to tighten a nut inside of the track guide is nearly impossible for the bolt within the actual guides triangular section. You can however fit a carriage bolt in there, and the nut on the outside.
As far as thread damage, on one of my cats nearly every bolt loosened with a wrench, but on the other one I had to cut off every single bolt. I think one was used to plow a parking lot with, and must have seen salt.