A couple of points to add to this conversation:
1. The Spanish did use iron musket balls early on, so finding iron in the
wound track would not be inconsistent with an incidence of gunshot trauma
for that era. A similar effect for modern weapons is referred to as "lead
wipe."
2. Generally, significant use of canister (picture a coffee can full of
balls) is attributed to Gustavus Adolphus's wars of the early 17th century.
Lead was widely used for canister shot up through the American Revolution.
Iron became the standard material in the 19th century. This would suggest
that canister might not be the culprit
3. Unfortunately, the article only shows one hole, and provides no real
description of the other. With gunshot trauma, the entry would tends to be a
more regular hole than the exit wound, so the little information presented
wouldn't appear to rule out gunshot trauma.
4. Would a crossbow bolt be able to sustain enough energy to puncture two
holes on opposite sites of a skull? When I was a kid (way back in the 80s),
I vividly remember seeing a news story about a guy in Kansas City who was
shot in the back of the head, accidentally, by someone playing with his
crossbow. The bolt entered the inferior aspect of the cranium, traveling
upwards to just barely poke through his right brow (supraorbital torus, if
you prefer), enough to push up but not break the skin. That was at a few
feet's distance, not moving through the entire skull. Surprisingly, he
lived, and the bolt didn't do any lasting damage (cue snarky joke here).
5. Stripped of so much context, it is really difficult to state whether the
person shot was kneeling, running with his/her head down, was simply below
the shooter on the landscape, or was lying prone and shot from a distance.

CGCD

-- 
Department of Anthropology
College of William and Mary
Williamsburg, VA 23187