The one about Thomas controlling Lara should be noted as impossible up to the point of Backup; since then is still open of course.
There's
mine, that Cowl is a human whose magic ought to be conditional, but Nemesis infection has made it not so. Which isn't very specific, and might be better expressed as "Nemesis infection can free humans from their half a bargain, while still getting the benefits." and "Cowl is an example of the above."
I've also theorised that Cowl is a former holder of the Blackstaff, but I don't have a good link for it.