You can remove the "censorship" with a 30-second config change. I don't understand why the people on that forum are so up in arms about something this trivial.
I'm not sure how much of a priority you think this is, but the one main problem I have with SageMathCloud is the lack of good documentation. Mathematica, as a counterexample, has comprehensive, searchable and easily accessible (just hit F1) docs. I humbly submit that including a way to browse and search documentation - not just Sage-specific, but also for every library it includes - would go a long way towards making SMC more usable.
It's a check - as of Android 5.0, Google's OTA updater scripts refuse to overwrite your /system partition if its checksum isn't on the known-good list. Rooting inevitably involves writing files to it, so OTA updates will stop working with an uninformative "Error!" in recovery. Whoever came up with the idea should be fired, but that's Google for you.
See [1] for details from the author of NRT [2], which can update your phone from factory images without wiping it. The procedure is a bit more involved if you're not on Windows - IIRC, you have to download the correct archive from [3] and modify the update script so it doesn't try to flash userdata.