The spec engine, or crate engine situation is a pretty good idea, but isn't foolproof. We run a GM #604 400hp/400tq 350 in our late model series, and we try really hard to keep it legal and in spec. Any work beyond changing valve springs must be done with a track rep there, and if your blown head gasket turns out to be a warped head, get out your Visa and head for the nearest GM store.
Problem is, most places that run crate motors allow, or even encourage rebuilding. We had a guy show up once this year, with a "guaranteed legal rebuilt crate" that was so obviously wrong it wasn't even funny. It fired instantly with that high compression bark, and made sharper noises than everybody else. I put the whistler on it- all the 604 crates I've tested are 9.5 or 9.6:1. This one was 10.9:1. I didn't bother getting the cam profiler out...