I think this will depend on the vigor/size of the tree combined with the size of the wound relative to that tree, but if you're coming from deciduous practice it's something like an order of magnitude less risky to cut flush regardless of which pine we're talking about.
I have not had issues with cutting smaller branches flush. But I've also never regretted leaving a stump and working with it the following year if the plan for that stump was to cut it flush. If you are the patient type and restraint comes easy, then I would say the only time I have actually regretted waiting was when the ultimate plan was to treat it as a jin, since it becomes much harder to work with the wood the following years. If you're not planning to jin or carve that stub though, then in my experience it's fine to leave it till the following year. But the smaller it is, the less that matters.
From a pine-beginner point of view, it is very reassuring to nibble away at a "left behind last year" stub with a spherical cutter and confirm with your own eyes that yep, every bite you make into the wood is revealing properly dead (brown) wood, and that this section of wood has been fully sealed off by the tree, meaning the risk of a sudden sap flow drop has now passed. If there's any life left in that stub, it might be at the base, and you'll keep nibbling until you find yourself nearly flush and ready to cut out a concave area and re-expose some encircling live cambium. If nothing else it is a nice way to gain understanding about what actually happens to that stub over time with a given pine and calibrate your personal preferences vis a vis stubs.
FWIW, regarding shore pine: I have taken big risks with both shore pine and lodgepole pine to the point where I'm convinced that you can go completely bananas with this sort of stuff. Never mind cutting branches flush, how about tearing off huge portions of trunks, strong/daring bends, etc. I've found these to be low risk as long as the tree in question is vigorous and you have strong foliage above to maintain sap flow where you need something to survive. Tiny shore pine buds that sit merely 2 or 3 mm away from freshly-carved-open trunk innards can survive on such a tree. So in that case, cutting a branch flush is very low risk. If you want to try daring moves like these, I would recommend that you grow a very strong sacrificial leader or sacrificial branch somewhere "above" the intended carving/flush-cutting area to keep sap flow past your wounds strong. And it may be wise to do risky moves like these in midsummer when you have plenty of runway left in the season for active/immediate healing.
