After a bit of messing about with the case, I worked out how it knows if its closed or open. Its the little magnet at the front centre. If you leave the lid open, and your iPhone on, you can trick the case to think its open or closed by holding a magnet to the top middle just in front of the headphones.
So, yes, I think that making the gap for the top of the airpods bigger would be ok as long as you don't damage the LED or cable, plus keep the magnet working.
I'm going to try just leaving the lid open all the time and make a magnet attachment out of sugu that fits will to "close" the case to charge.