FYI, trainer/instructor Rob Pincus has his magazines the same way in some of his videos and he has the same arguments as the OP. I'd say use whatever works for you and stay consistent with your reload method.
Index finger is great but it won't work for everyone or every method. Take a horizontal mag pouch for conceal carry, for example (Safariland model 123). I'm hoping to add this to my CCW rig, as well as use it for IDPA