The likes of Fender, Warwick and other recongnised brands don't seem to find a problem with it. Why should custom shop instruments be exclusive to endorsing artists? If your passionate about owning a specific bass built to your specs, dipped in adamantium with meteorite inlays and are willing to pay for it, I don't see a problem - and nor do other brands.
It smacks of EBMM being elitist.
Owning a custom shop isn't just about promoting the brand, it's about owning the instrument of your dreams. If you build it they will come, unless you're EBMM, and they won't come.
EBMM has decided that it's not financially feasible to offer a custom shop. I don't see that as being elitist. Simply ramping up the custom line would cause an impact in the normal production line.