I think you should probably plug the tuner holes, veneer the headstock, and drill it as a 3+2 instead of a 2+3 headstock. The tuner bushing is going to hang over your truss rod access, and there will definitely be problems with a truss rod cover.
I tried doing the 3+2 layout during the design phase. It wasn't happening as I couldn't get the straight string paths. But you're right about the truss rod cover. That won't happen in its current state.
