I have all the receipts for the build. According to the owner (who posted here, over in the NorCal forum), ERA delivered a roller, Danbury delivered the engine, he bought the trans from somewhere then he assembled the whole thing in his garage. So I'm good on that point.
I don't see where a specially-constructed vehicle is subject to the other new-car requirements (e.g. 7500 miles - which appears to apply almost exclusively to new cars that are 49-state smog legal but not California.
AFAIK, Fed and CA smog have been completely in sync for many years - you have to go back to the 70s to get into things like 4-speed TransAms that couldn't be sold in CA. I don't see where, for example, I could register a 2006 Mustang with 7,501 miles on it that has had the smog gear removed. It appears to be all about that 49/50 state thing and the vehicle still has to pass year-correct smog testing.
I also have found no trace of the option to register without an SB-100 exemption. The engine is a 1966 date code, but the body and completion is 2006, meaning that it would have to pass current smog limits to qualify. It could have a cam smooth as a glass ball and that wouldn't happen. :P
I'm going to try speaking with DMV today to see if I can get any clarification. In this time of cutbacks and furloughs, I don't much expect to get anyone knowledgeable...
Thanks for the further input. G'damn, this is confusing.