I think so also for certain now we see it.
On the pickup being raised, I assume the proper height is more of an expectation of height rather than it would not work lower with the neck angle as designed?
Unless I misunderstand your question, the pickup height (from bottom of the string to the top of either the poles or the pup case itself) is a function of pickup design. Some pup designs do have a greater range of workable heights. In any case, all pups do have a "sweet spot" that produce the best/proper clarity along with tone and output.
Filtertrons (at least original spec design and TV Jones equivalent - including these Brian Setzer issue) are particularly "finicky" with respect to the range in which they work. In this particular case (TV Jones Brian Seter) the bridge works pretty well within approximately 3.5 and 4.5 mm (
Note: TV Jones recommends 5/32 inches (4mm) between the top of the cover and the bottom of the E strings on the bridge pickup). I happen to agree with TV Jones on the 4mm (5/32") recommendation. (again - just my limited experience).
On the initial setup, I had almost 7mm of gap between the pup and the bottom of the E strings (and that was with the adjustment screws fully unwound). Long story short, I decided to shim the base of the route to allow for the best height adjustment range possible.
When I compare the neck break angle and the height of the bridge to my Les Paul, they are very similar. So based on that and the general expectation on fixed bridges (since Warmoth is doing this to accommodate most setups) and noting that both the Les Paul and the Mooncaster bodies are carved tops; I get why they programmed the route as is. However, if the route were made with slightly less tilt back, the bridge (and pup route for Filtertrons) would work out MUCH better.
I'll provide some close up pics (and comparison to my LP) to show you what I mean.
In no way am I dissing on Warmouth. Again, I think I can understand how they likely have a very set "CNC program" for the neck pocket route. I would just suggest that - as in my case - when the custom order includes the particular combination of the Gotoh 510 wrap-around bridge (which I got from them and is one of 2 selections in their build list) AND FIltertron routing, they could adjust that routing program to reduce the angle by a degree or two.
Just to complete the thoughts I've had on this... I've also considered reducing the thickness of the "sole/shoe" (the place where the neck bolts to the body) by sanding it down a bit to lower the neck; and/or creating a bit of a negating compensating angle to that such that the net effect is to reduce the neck angle. But it's really not necessary (and probably not the best approach), given how easy it is to just shim the bridge pup pocket route.
Follow up FYI.... I decided to calculate what actual delta the angle had to change in order to bring the bridge/string height down to a "reasonable" height (meaning - what would work well/best). So the angle would need to decrease by 0.8 degrees (so assuming a 4-5 degree angle) would bring it down by about 3/8" from it's current height