As long as you don’t touch the first 32 MB’s on the eMMC, uboot should be fine. It’s located in those. Not in any partitions.
As that amounts to around the first 32 MB’s, then yes. See above answer.
The files in /boot, are provided by the uboot package and are only used when you need to flash a new uboot to the drive. They are not used to actually boot the device. Your NVMe install also has these files in it’s /boot.
Well, you can just change what drive gets mounted in your fstab and you should be safe.
In newer images, we use the PARTUUID in both fstab and extlinux.conf, to avoid exactly this issue. 