considering PopOS is trying to tackle Ubuntu they really need their dual-boot setup to be a lot less tedious

The part where you want to add 2 EFI partitions is not advisable. It seems that Windows doesn't really like this, of you are dual booting multiple Linux installs it might work. But it is always recommended to use only 1 EFI partition per disk. Hope this helps. :)

You don't necessarily have to resize Windows' EFI partition. You can have multiple EFI partitions.

Make a 512MB fat32 partition during manual/custom PopOS install.Select its role as: "/boot/efi" in the PopOS installer.When the OS is installed, type sudo apt install refind and then it should automatically start the installer else type sudo refind-install. This will install rEFInd to your /boot/efi path.