It wasn't just Chrysler that used to recommend that they not be re-used. It was pretty much the universally accepted recommendation for both the flywheel and ring-gear bolts, for many many years.
That said, I've gone against instructions many times too and re-used them in both applications. On the diff gear though, most complete rebuild kits come with new bolts anyway, so going new is an easy decision.
I'm sure there's a very good reason that the manufacturers recommend that kind of thing, but so many have done it anyway, you should be fine, like the others have already said.
They probably say these things because their lawyers have already learned that we're going to re-use them at least twice anyway, but with the warning in the back of our heads, maybe we'll at least get new ones on the third go-round?
Paul