It's an interesting point and I've now looked back at both songs route to the final.Not that it will matter and neither should it in a head to head but the Boxer received significantly more votes in the lead up to the final than Gimme Shelter.
As you say, The Boxer has amassed more points total, but in terms of opposition and the songs/bands that Gimme Shelter has beaten, I would argue this song has had a tougher route to the final