Interesting.
I get the impression that doing the angle on the neck pocket is easier in the end. Done at an early stage of the project, when you still have a flat surface where to mount your pocket template, it's just a matter of angling the template accordingly.
Usually is what I do. Later on, only if I need a minor correction on the angle, I adjust the neck tenon.
But the truth is that as long as your angle is not too dramatic (only applicable to full neck width tenons, anyway), you should not have any problem with either approach.
Perhaps I should elaborate. So far all my builds have featured long tenons (10"-12"). These have a pocket routed into the body to a uniform depth--the same thickness as the tenon. The neck is set and the tenon is machined flush with the top surface of the body. Then the top is glued on. Putting the angle in the tenon seems the best way to achieve that construction.
The relevant point is the same as you made....it works just fine, and also like you said, it must be full width as well.
SR