The paint on this joint sometimes cracks due to the expansion and contraction of the spot welded joint. The roof is spot welded to the quarter panels and A pillars but is sealed with lead at the factory..
IMHO, you could weld the joint and cut a fake seam, but if you are off just slightly with the grinder, could cut into the thin sheet metal, missing the weld and cause yourself more work. I would lead it in and just scrape a seam over the joint with a file which would not cut into the sheet metal.. It's what I do..