LineageOS OTA updates are not incremental, they are complete OS installs on the unused OS slot, so it seems comprehensible that any low-level tweaks will be overwritten.
If you could get Magisk to survive, I think your best bet would be if Magisk modules would apply those tweaks and reapply them automatically after updates. I’m not running Magisk, though, so I wouldn’t know.
Perhaps here’s something … Feedback from usage of LineageOS on Fairphone 3+ - #12 by Woaloo.