Cut them down so the sides are not as high. I just use a pair of scissors to do this, it gives the egg enough room but still supports them. If I get chance later I will take a pic of what I do.
Cut them down so they are shallow. Trim the sides of the cartons down. That's what I did with these in the pics. These are small polish eggs so not a large egg barring the brown egg that was a mutt egg.
Yes unfertile eggs will still have a degree of air cell growth as the egg loses moisture. Eggs just sat on the counter for a period of time will lose moisture too. It's a natural process as eggs are porous.
If you are unsure of development leave them in just incase.
I have hatched a fair old few, my top tip for you is to read this ~https://www.backyardchickens.com/a/hatching-eggs-101
It's a bible when it comes to incubating and hatching!!
Here are a few pics ~