just get two humbucker routes, and try the bass pu first, then if you like it, make a third third route, or get all three if you plan on getting a stat, or something that has a pick guard. it will all work together, id suggest going with an 18v setup, and it would be cool to use a preamp in conjunction with the bass pup, and some emg guitar mods with the 85 and 81, like an afterburner or a phase shift. or a resonants cut or boost.
they use regular guitar pups with a baritone, so i don't see why a bass pup would hurt, and les claypool has a super narrow neck 6 string bass with incredibly light gauge strings, so its pretty much one step up for a baritone guitar, and he has emg bass dc's in it.
i always wanted to get a super long scale baritone with a wide neck, put ultra heavy strings on it, tune it like a six string bass, and use bass pups.