Oh my...a good question indeed!
I have only built modified and/or custom designs (electrics I mean) so I can only speak from limited experience, but here it goes.There will be some differences between a bass and a regular guitar (er, 6 string...er, whatever you want to call it
) The body will need to handle different stress levels/loads, the electronics will differ and the scale and neck dimensions will be longer. Other than that, I am not really clear on any massive differences that will effect your learning experience. One thing to keep in mind...bass players tend to be more forgiving of radical design changes and experimental looks/feels. Browse through the messages on this board and you will find some fantastic, and different looking basses. Regular guitars? Not so many weird designs out there.Oh...keep in mind, the school may 'inform you' as to what you will be building.
Again, this is totally my personal taste, and from a rather limited experience perspective, but given the choice I think I would do a bass with an experimental design or a traditional 6 string (Les Paul style maybe?).
-Matthew