The spalted caps are very thin and easy to sand through, so generally you want to do as little sanding as possible. As such, the dye black and sand back could be risky, but others can provide better advice on that. Andrew has had some good success with ebony Timbermate on his spalts.

Doing a 'one piece' clear finish with the neck glued in is certainly an option. It looks great and provides a more seamless outcome to the finish. But, once the neck is glued in it is:
- much more difficult to handle, hang, and manipulate the guitar when finishing.
- more challenging to use different finishes/topcoats for neck and body.
- more difficult and damaging to the finish if the neck ever needs to be removed.
- more problematic if final adjustments are required once the hardware goes on, neck angle tweaks etc.

But, it depends on the finish you're using, the look you're going for and how confident you are that you'll get everything right. That's just my opinion though.

By the way, that is a good looking cap. I don't think we've had any roaring red spalts, should be awesome.