How so? The bootloader only boots what is in the boot partition, it shouldn't even care about anything else if it's properly unlocked. The only issue on standard AOSP is that encryption there affects the entire 'userdata' partition, so the OS must manage to boot and prompt for a password while only accessing the "system" partition, which is relatively small on many devices. But that's no different than booting a system that has had its userdata wiped (either as part of bootloader unlock or for recovery).
So which of the Linux distros that run on Pinephone do support FDE with LUKS?
That said: Yeah, Android+Linux is super weird if you're used to GNU+Linux:) And I'm pretty sure it would be more complicated, since I'm basically proposing that we protect data but not code; I think you'd need to protect /data at a minimum, maybe more (I forget where Android sticks the "internal storage" directory). That said, I think you could do it on Android.
[0] I was going to say GNU/Linux system, but pmos is based on Alpine which isn't really GNU so much as Busybox/Linux...