I can guess that the reason they upgraded stim patches to 'remove' from 'ignore for wound modifiers' was that stim patches didn't actually help you stay in a fight longer, which is kinda what they're supposed to do. Popping a rating 6 stim patch at 9 out of 10 stun boxes filled was practically worthless. You'd get two dice back, but you'd still be taking a nap if someone brushed past you a little too hard, since a 10th damage would fill your track and knock you unconscious.
Removing the boxes means that you're still in the game for another 7 stun damage.
Mage-wise, keeping with the 'no non-natural healing' I'd say that it's pretty clear that stim patches are in the 'non-natural healing' category.
If you read the description of First Aid on p205, that even says:
QUOTE
Each net hit over the threshold removes 1 box of damage
So you can't really rules-lawyer your way around there being a distinction between "heals damage" and "removes damage" as the rules tend to use those two phrases interchangeably.
Thematically, mages are lucky they can use stim patches and trauma patches at all in this edition. Used to be that emergency first aid was a short bus ride into burnout land.