Download the Stock Rom from here and SP Flash Tool just in case you need to reinstall Stock. Download a system image, note you need to use an A/B arm32 image with 64 bindings. For example AOSP 9 is here.
This process probably can be done with SP Flash Tool but I wasn't able to manage it due to the disable-verification flag required.
Unzip the stock ROM and reboot the device to bootloader, connect via USB and unlock via:
sudo fastboot flashing unlock
fastboot --disable-verity --disable-verification flash vbmeta vbmeta.img
fastboot flash boot boot.img fastboot flash recovery recovery.img
fastboot flash system SYSTEM.img
For root install magisk manager and you have to patch the recovery to get root (not just boot as flashing boot alone doesn't give you root). So in magisk get it to patch you boot and recovery images and then put those on your computer, go to bootloader and use:
fastboot flash boot magisk_patched_boot.img fastboot flash recovery magisk_patched_recovery.img
To get root then you need to reboot to recovery, hold power button + volume up and select Recovery. This will appear to boot as normal but you will have root when you do it this way and not when you boot normally. Unfortunately I do not have reception when I do this but do have root, other users have this problem but I have not found a solution.
Note that I thought I bricked my phone a few times before getting this as nothing would happen after a failed boot and I couldn't switch it on, however what happens is you can't do anything until the battery has almost completely discharged, then when you hit the power button you'll get the no battery sign and when you plug in you can get to Recovery again. This is quite annoying if you've charged it quite high as you'll have to wait a long time to discharge and be tapping on the power button a lot!!
What doesn't work
Battery usage doesn't work, this can probably be fixed following this guide. If I get time I will attempt this.
Other things to note, there is no TWRP yet so I don't have decent recovery options, this also makes it harder to use certain ROMS as you can't flash things like gapps if you install a ROM without it.
The battery life if definitely worse using AOSP GSI than stock, maybe that vendor overlay would help with that though.
I hope that helps others.