tl;dr - you need the headers if that window is in a span of more than a few feet in any direction. That section of roof will probably never collapse, but it will definitely sag over time and create leaks around the skylight, which will lead to mold and water damage of the structure and your belongings. Call them back to finish the job properly.
Explanation
The section of roof above the cut rafters, both in view and behind the camera, no longer has end support, so it is hanging from the adjacent rafters. These now have carry roughly twice their original load. An engineer would have them go beyond headers and first install "sister" joists to the uncut ones on each side, as would be done if this was a new build (along with metal hangers at every connection).
While the deck sheeting does spread the load out enough that the severed section won't cave in, it is much weaker under vertical load than joists, and will bend differently from the rest of the roof. Over time* it will gradually warp out of plane without the missing joist support, especially with the heavy snow load and seasonal temperature swings in Toronto. The differential flex and/or sag will eventually breach the waterproofing around the skylight, and if the got bad enough, the displacement could impede the window's operation or even crack it if the frame was sufficiently squeezed or twisted. Perhaps under a record snowfall while you're away on vacation.
*months to years to decades, depending on the sheeting, surrounding framing and spans which we can't see, etc.