As far as HSS flare groove root opening is concerned, I would think that you would need to measure the distance between the faying surfaces of the tubes, or sidewalls, at or just below the radius line of the larger radius, though I can't supply a code spec or diagram to confirm.
AWS requirements for flare groove joints are vague, and leave too much open for interpretation, IMHO, which causes me a lot of grief.
As far as whether the weld has to be flush on the surface or not, I think the only way to accurately define that requirement is for a flush contour symbol included with the weld symbol, or a below flush detail included in the tail of a welding symbol or a drawing note. The purpose would be to head off possible differences in opinion during visual inspection.
Here's a link to a past discussion on this:
https://app.aws.org/forum/topic_show.pl?pid=280695;hl=flare%20bevelTim