So I enabled com.onyx and onyxotaservice, update twice with upx files and flashed boot image again.
All seems good, however:
1) Developer options were still inaccessible. I had to create new user with pm, switch to it and back with am command, and it did the trick.
2) Gestures are not working! Neither bottom swipes nor side swipes (new in 3.1 to control light and warmth).
3) I copied over Magisk modules from backup (because I deleted Magisk once in the process). However, modules don't work most probably due to permissions.
4) Due to (3), SSH still doesn't work, now it doesn't even want to connect. Before it was just rejected key.
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