Scenario 1.
Easier way is to update Oct OTA from current slot and reboot . See if you are successfully booting up and you should be unrooted now. Then go into fastboot, fastboot boot boot.img(Oct cf auto root img) . Wait for it to exit fastboot. This can take few mins..once booted up flash fire will be able to get root access and you can inject supersu via that and profit.
Scenario 2
If you update Oct OTA from your current slot and you get error. Then boot into fastboot and type below command
"Fastboot set_active x" (your other slot a or b)
If above doesn't work, then
"fastboot --set-active=x" again here x is slot you have to change to.
Once you have changed slot successfully, then fastboot reboot..
Now you'll be in unrooted slot. Update Oct via this slot and it should go through without issues.now your other slot which is rooted is also updated to Oct. Now make slot b active via fastboot.
follow same fastboot boot boot.img and get root access and flash su via flash fire. Done.
So for every future update your slot which is unrooted is available for OTA and you can root the rooted slot by cf auto boot.img..peace..
How do you know which slot is currently active?
And If I understand your scenario 2 correctly (and decide to skip to step two to not risk no-boot scenario) - > boot from the other slot, install OTA normally, change slot again and boot, then launch the auto root thing script, done ... right?
The thing i dont understand - you said that if you install OTA over your currently rooted system and it doesn't boot afterwards, you change the slot and install the OTA again - how is this gonna make the first slot boot? Confusing.
Or could possibly this scenario work (in theory it seems most simple):
(current rooted sep version): 1/ downloading incremental OTA files - october update 2/ flashing the OTA incremental with miflash 3/ system should be now unrooted october (will it actually boot?) 4/ running this root script 4/ rooted october system. Or am I wrong? Also, will flashing the incremental OTA relock the bootloader?
P.S I rooted the september version using the CF auto root method without actually installing flashfire or injecting supersu - just ran the script as posted and the phone was rooted after reboot ( I just installed supersu from playstore afterwards). Why the two methods if the "simple" one works just fine, can someone explain this to a noob? Sorry for lots of questions, but after reading about this in several topics with different approaches, it becomes confusing .. and i dont have the time to spend all day figuring it out the hard way and bricking the thing doing it ..
Cheers!
Jaka