I'm probably going to be unpopular for asking this, but if you don't even know what size drum you want, why are you going custom? Ask yourself what the custom build route can deliver that the standard series from a range of manufacturers can't.
If you're getting someone reputable to build your kit, ask the advice of your builder. If he/she's good, they'll be able to guide you based on the information you give them. Tell your builder exactly the sound you're searching for, & see what comes back. The reason a good builder is the right person to consult on this, is because drum depth is just one of many design elements that must be considered together. For example, a 20" deep drum on a very thin shell is likely to overload the overtones to the point of confusion. Such a drum will be very muddy in certain applications.
The same advice goes for all the drums in your proposed kit. Consult your builder on all these subjects. If they don't have the expertise, or you don't want to take on board what they're saying, then move on to another builder.
One little point to take into account, a deeper shell bass drum does not automatically deliver more low end. It very much depends on the construction & other factors.