Create hole in shoe? Modify toe?

Use a sharp knife to cut the rubber careful not hit the leather, utilize a shoe stretcher to get to final result if needed. 

Update: luckily after about 30 gym sessions the left shoe has stretched sufficiently, and the weird bump seems to have permanently lost feeling. I may even consider trying the 46.5s out again now that I know they will eventually stretch.

Yes, you can certainly do this. My second toes are longer than my big toes, so I often have to create little holes for my second toe knuckles to sort of leak out of. For routes with extensive foot jamming, I just where bigger shoes that don't have the modification. I haven't had any issues with the hole (in the leather parts) getting out of hand. Go for it. Comfort matters.

I sometimes size up and wear socks, helps a lot for long days. Plus they stink less