BTW, fantastic project! Impressive that you are trying to innovate.Iterate, iterate, iterate!
Agree that ixconnects aren’t the standalone solution here, especially on the top and bottom body sections. Clamex connectors will be virtually flush on both mating pieces, which is definitely desirable for the user. So Clamex pieces make a lot of sense when connecting a section as long as 430mm.
IMO, your approach to attaching/stabilising the neck with a metal truss rod running inside the neck is sound. However, you could mitigate welding on connectors by supplementing the connection with Ixconnectors, for example.
Agree that dowels in wood might eventually succumb to movement. Therefore, for the upper part of the fret board is there any benefit to using a really stable material such as Trespa/HPL? For example, 15mm thick HPL laminated onto a rounded off ash/tulip fretboard backing? If the neck connection were lap joints (with the top part of the lap being HPL) then 2x Ixconnectors in this part would be guaranteed to be stable, and the lower part of the lap (in ash/tulip) would house the metal rod. Whereby the rod would be purely for tensile strength, as the Ixconnectors would “pull” it altogether? No need to weld anything on to the metal rods - just friction fitted.
..Just more food for thought ;-)
Good luck