I just wanted to say to @Juulll here since the thread was locked, I just upgraded from 17.04.1 to 17.09.3 about an hour ago, on an encrypted phone with no system modifications, and it went just fine; very fast installation after downloading about 330MB and a slow boot & optimisation as to be expected.
However, when the phone booted it froze up as soon as BetterBatteryStats tried to ask for root permissions (as in, no physical buttons responded and the screen was frozen though it displayed a spot where I touch as per my usual setting, but nothing responded to that touch input). That app was definitely the problem because two other apps both got their permissions without a hitch.
So, on reboot I very quickly went to F-droid and uninstalled that app, and now it seems to work fine as far as I have tested. So take that as a warning to un-install BetterBatteryStats if you have it before upgrading to Android 6, as it seems to have some serious compatibility issue.
17.10.1 did not appear when I launched the update app about an hour ago, although it might not have checked for any updates, but the device has been on all day with an internet connection for nearly all of that time, so I would have hoped it would pick that up. 
Edit: Found another big problem with an app & A6.0: Trying to connect to my WiFi produced the errors “Connected, no internet”, “Wi-Fi Connection Failure”, and eventually “No Internet Access Detected, won’t automatically reconnect.”.
This seems to be because A6 no longer allows an app to see a list of network connections without Location enabled, meaning that the app Wi-Fi Privacy Police could not see that you were connecting to a trusted network without allowing all apps to know your location. Also see the issue with pings to google’s server’s that I found in the article linked above. Fuck you, google.
I feel a bug report brewing, but I need to sleep first.