First of all, it's generally good practice to NOT store leather boots in turnout pants – when not done carefully, the pant legs often put pressure on the sides of the boot, bending them over and changing the shape of the boot. When you wear a boot that's been flattened, the fit may change and become uncomfortable.
That being said, as long as you make sure the pant legs aren't pushing at the tops of the boot, it is possible to store them within turnout pants safely.