The warranty on the Stigmata is
not dependent on the LBS. Just register the bike with Santa Cruz.
I would pay more attention to a shop that actually has it set up correctly when it arrives. I got mine at Summit bikes and would never recommend going there after that. I had to re-do the hoods on my bars because they were askew and a crank arm fixing screw was not properly tightened.
I'd go through Mike's Bikes. They are now owned by the company that owns Santa Cruz and, while they are not my main LBS, they have been friendly and competent ever time I've gone in for something.