I thought about that... Actually there is already a negative battery cable running under there. No junctions of course, but besides that, the frame rail was pretty clean. I was figuring to wrap the fuse tightly to make sure it was vibration isolated as well as fairly water tight.
Do you think this is a **bad** idea, or just an untested one?
I personally think that it could work fine. I'm not sure what you had in mind for conduit, but sliding something like some PVC pipe over the fused area (so even if the heatshrink, tape, etc took a dump, there'd be some insulation) would work decently, I think. You might even be able to get end caps for the conduit and drill out the diameter of the cable so it's as sealed as possible.
Let us know how it works out.