How close to the bridge the bridge pup is and how far from the neck the neck pup is. Affects each pups sound. With guitars the neck pup is normally right up next to the neck. Hence you get a slightly diff sound from gibson scale versus fender scale guitars that are otherwise the same. With bass guitars though the neck pup is normally more like 1 and 3/4 to 2 inches away from the neck. For soapbar pup basses anyway. If the bridge pup is too close to the bridge it can cause overly treble oriented voice even with bass heavy pups. Hower, you ussuallu dont want the bridge pup to far away either. Or it starts to take on more the char of mid position pup youd have on a 3 pup guitar, or like trad P pup placement.
If your going with J pups, their narrower nature will make distances from bridge and neck a bit longer. Also in some cases, slanting them so one side is closer to the neck and other side closer to the bridge. This gives a little bit of that offset sound P pups have with their two halves where one side is closer to the bridge.
Id suggest talking to the builder about what your wanting to accomplish bass voice wise. To help you select pup placement. For example if you decide on P pups. You may find it suits you better to have them positioned reverse. Meaning the E&A string side is closer to the bridge. Rather then the more traditional opposite of D&G tsring half closer to the bridge. You should allready know what your fave pup type is. Soapbar, P, J, or humbucker (the giant ones with large exposed double row of pole peices). For both neck and bridge position. This can be two of same kind or any combination of 2 diff ones. You might for example decide to go with a soapbar bridge pup and a slanted J neck pup. Or even reverse positon P bridge and humbucker neck. Odd though those two weird example might seem. Lol. The more common would be two of same kind or a P & J pup setup. For bridge P pups I think it sounds better to have the D&G string half as the further from bridge side with the closer half at least 3/4 inch away from the bridges front edge. Though haveing D&G string half as the closer to bridge side can work fine if again its at least 3/4 inch from bridge and preferably a full inch. Imo.
If you look at various boutique basses along with Warwicks. You'll notice the pup placement is sometimes not the same as on most production basses. This is cause the maker and customer liked the tone tweak these shifts to pup postion gives. It has to do with both treblier/bassier sound and how other parts of the freq spectrum of the note are accented at various distances from the bridge. Its not a big difference, but can make for a nice or not as nice sound tweak. So again Id suggest discussing with the maker what youve liked and disliked about pup placement on various basses youve played or owned. And together decide what shift if any, from the common placement. Your pup installation will get. Part of what makes custom custom basses so unique is this greater customer and maker interaction to get the thing as close to dream bass reality as possible. Or perhaps even surpass it.
Maybe some of the pup and bass makers will chime in with their take on pup positioning & some starting measurements for the various pup types soapbar, P, & J.