Custom drums can be divided into 3 catagories IMO.
1/ Mass market manufacturers who offer a custom size/finish service. To be honest, I choke at the premiums that are charged, but I'm not surprised. I run manufacturing operations, so I'm fully on board with the costs incurred when interrupting production flow/inserting a special into the system. Unless they operate a dedicated custom division within their facility, the stop/start costs are high. In most cases (Sonor SQ2 being an exception), you get the size & finish you want, but the basic product is stock.
2/ So called "boutique" custom shops (i.e. Spaun). They use shells made by others (e.g. Keller) then work the drum up from there. Here, you typically get a bit more choice. Some (not Spaun) will offer different bearing edges & lugs. All offer a choice of hoops, tom mounts, etc. The value is in the choice, quality of build, attention to detail, & service.
3/ Custom shops that build their own shells. Here, you usually get ultimate choice, & a true bespoke kit. They offer the opportunity to truly craft a specific sound. To me, these represent the very best in drum building. Most surprisingly, they can often be cheaper than either the custom facility of a mass market manufacturer and the "boutique" builders. This is usually down to their small size/lower overheads.
I have a Spaun custom series maple kit. It's superbly made. No complaints. I'd happily put it up against any DW & expect it to sound better than most, IMO. I'm currently having a very unique kit built by Dean @ Guru Drumworks
http://www.gurudrumworks.co.uk/ This project is leading edge stuff, & made by a true wood artisan. We are collaborating on a design build that's way off the accepted path. You only get that level of willingness to experiment from a true enthusiast. Although the cost will be high, compared to the prices DW charge, it's exceptional value for money considering the huge amount of development time & work involved.
A UK company such as Highwood drums make beautiful true custom (catagory 3) drums at very realistic prices. Of course, there are others. Do your homework, & you'll find that custom drums don't necessarily have to be crazy expensive, & the can represent superb value for money for those seeking something very specific.
I often ask the question the other way around. How come some of the mass market kits cost so much compared to stunning custom kits? The answer is usually a combination of brand recognition & overheads.