How can I check from the boot section that the App.hex file I just updated is correct?
That can be addressed via the bootloader and its controlling app on the pc- such as reading the flash after its programmed and compare it to what it should be. So if you want to only verify programming and do not need verification on each power up/reset, you could skip the boot crc checking (whether using hardware crcscan, or on your own).
According to your posts elsewhere-
https://www.avrfreaks.net/s/topic/a5CV400000000HlMAI/t393167?comment=P-2934502IAR can generate the crc for you, but you would have to come up with an initial value due to the bootloader code being included in the hardware crcscan. You could also do your own crc checking code in the bootloader where you only check the app code and could then use the iar generated value with a default initial value.
Unless there is a real need for crc checking on each power up/reset, or even while running (pretty hard to otherwise detect corruption if your app remains powered on for long periods), I would stick to only verification at time of programming which is easily done by any bootloader/pc app combination (and most likely already done).