IMO they are not boutique, DJ are cheaper than Fender MIA and Sadowsky Metro did not offer you any option.
I have own both DJ and Sadowsky PJ, I like both, DJ is $1000 cheaper and honestly the only difference I noticed was the sadowsky pre amp, its worth $1000 , hell not
You are confusing the term 'boutique' (meaning, in general, coming from a small company usually with the founder of that company still in charge) with 'custom'.
I agree with you, neither of these basses or lines are custom, but IMO they are boutique, versus the thousands of basses that a company like Fender puts outs. I'd personally rather give my money to Dan Lakin or Roger Sadowsky than the 'Fender Corporation' at this point (assuming I like the basses... which I do!).
Regarding if the Metro is worth the extra $1,000, my guess is the Metro owners would say 'yes' and the Skyline owners would say 'no'