Hey everyone. I haven't had an account here in a long time but I saw this thread and felt that I needed to chime in on this as Mas worked for me a long time ago. For a quick background, I worked at Manny's Music from 1997 until 2005 and then I had my own store, Guitar Man from 2005-2010. Mas worked as my repair man for the last couple of years Guitar Man was around and he also did some of his building in my store.
Let me preface this by saying I haven't spoken to Mas since sometime in 2010. He was mad at me over the way my store went under though that was a complicated situation and I had left the business before my former partners shut it down. Though I would have liked to have explained to him my side of the story but he never gave me a chance. And while I have no real reason to defend him, I also know the way he worked back then and may be able to shed some light here.
First, while Mas was working for me he never cut his own necks and bodies (and neither do a lot of boutique builders but we'll get into that). He ordered rough cut necks and bodies from (I think) Musikraft at that time made to his specs but he would then hand shape them as well as install the frets and so on. I do not remember what he did as far as finishing the bodies (whether he sent them out or did them himself) but everything else was done by hand by him. And while I have no idea what Mas is doing now (or I guess was doing up until his accident), I would imagine he was doing something similar with the Warmoth necks and bodies.
Second, a boutique bass is much more than someone just assembling parts. You're paying for the time put into making that instrument as perfect as it's going to be. You're not talking a few hours. You're talking a significant amount of time and expertise. And that's really the difference between a mass produced and a custom instrument - the time put into making it.
Third, I'm not going to out anyone here but lots of boutique builders outsource their necks and bodies - not everyone has the facilities to cut their own. Anderson Guitars used to cut the necks and bodies for Sadowsky and Pensa-Suhr when they were a smaller brand just as an example. And Warmoth cut them after that. Lots of small builders outsource their necks and bodies, while others make them in house. At the end of the day, as long as it's good quality wood that has been properly dried out, does it really matter who does the rough cutting?
That said I also see where the OP is coming from. I would be weirded out for sure if I took the neck off and saw the Warmoth logo. And I also find the headstock odd and that's a bit of a flag to me. Unless Mas changed it so that it's less neck heavy or something, I don't see what the point of changing a headstock you're know for is. I would think if he had changed it for a reason he might have said something about it but at the same time maybe he didn't want to freak out the folks who have his old headstock. Unfortunately Mas is the only one who can explain that.
So that said I hope this sheds some light onto the situation. I'm not in the business anymore and I really don't know what Mas's newer instruments are like but he is one of the best luthiers out there and I would like to think his work is at least as good as when I knew him.