Android keeps loosing Launch Defaults, app settings and installed updates and installed apps after every reboot
The root cause was a wrong edition of TWRP: I mistakenly downloaded TWRP for Titan series of Moto G 2, while my XT1079 phone is obviously part of Thea series.

Discovered that through trial-and-error in several other re-installs of the original ROM, GApps, TWRP and OTAs.