OP, you definitely need to make sure you have a supportive footbed first. Without a footbed, your foot naturally falls into this portion of the shell. So, it is highly likely that using a supportive footbed will alone solve the issue, as it will not allow your ankle to travel inwards toward the medial side of the shell.
Furthermore, if you stretch this area and do not have a supportive footbed keeping your foot in place, then your ankle/navicular will fall into the space that was made. Stretching without having a footbed is rarely successful because it does not solve the problem at its source.
So you should proceed in this order:
1. Get a supportive footbed to stabilize your flexible foot so it cannot fall into the shell due to its own movement
2. If that on its own does not solve the problem, then have your boot-fitter modify the shell in the area that hurts