The 3x3 headstock is smart thinking (normal guitar strings are long enough to be used as trebles if need be).
Assuming you're OK with standard guitar spacing at the bridge, the biggest hurdle seems to be the stopbar, and at least this one
GE101Z-T - G-GOTOH
has .118" wide holes, so it would work. (I mean, ball ends may not sit perfectly in their sockets depending on specific size, but the "problem" would be only cosmetic.)
What I would do, in order not to be married to the not spectacular variety of available bass VI sets, is
- place the stopbar at the right length for usual VI sets (whose length is actually in the "medium-scale" bass string ballpark);
- drill string-through holes directly under it, which would allow you to use long-scale sets (which are waay more widely available).
In addition to that, I would consider a wraparound bridge with adjustable saddles instead of a regular TOM. They have a wider intonating range (saddle travel + "pylon" screws). Heck, I'd even look into whether they have holes wide enough for bass strings: if so, one could even throw in a short-scale string set on short notice!
[Easier than the above would be a short bridge to bar distance, and an inline but reverse headstock: short, medium and long scale strings would all fit no problem.]