I installed /e/OS and Magisk this way:
- Install /e/OS
- Install TWRP as described https://twrp.me/fairphone/fairphone3.html (“Fix Recovery Bootloop” was not necessary, it threw an error but the phone works correct)
- Flash Magisk ZIP from TWRP (no boot.img patch needed)
For OTA updates I follow this tutorial https://www.droidwin.com/install-ota-rooted-android/ (but Step 1 is not necessary with /e/OS because it does not check for unchanged boot.img but simply overwrites it). So I just begin with step 2.
I did it this way with several OTA updates and everything works correct.