I've seen a lot of bikes with this sort of configuration. Given the thickness of the shell and the anticipated movement of the shift cable (i.e. very little) I can see no way that this configuration will compromise the condition of the shell. Before the under-shell routing, we had brazed on clips above the shell. Even though they are much thinner, I've never seen one of them cut through by the cable.

Just ignore and consider it part of the vintage experience