How important is it that the shoulder pad is perfectly flush with the armhole?

I actually find setting of the shoulder pads to be quite tricky, at least with the drafts I use for my own garments. I have found it can depend on shoulder seam slope - as well as the length of the shoulder seam (ie. narrow vs. broad shoulders) - which serve to define the final angle of the armscye in relation to the shoulder. For me, the solution is to set the shoulder pad so that it corresponds to the armscye at the front and back shoulder pad tips, and then to rotate it outwards until it fits snugly inside the shoulder region. This invariably results in excess pad which protrudes at the top of the armscye, and this needs to be trimmed off.

So, to answer your question: in my opinion it is important to have the shoulder pad extend completely to the seam along its entire length, but the way of achieving this is to ensure it fits correctly with excess and then trim it to shape.