Actually after further investigation, it appears it was only my personal machine that was affected, more than likely something I was doing alter its state. LXLE however even after applied updates seems to unaffected in either version, so it looks like it was an isolated issue with my machine only not lxle in general. Sorry for the confusion and unnecessary alarm.
The unattended upgrades is only for automatic security updates. It will not install any updates that are not classified as such, I checked on a freshly installed 64 and 32bit machine and both weren't affected. Perhaps something we both do on our machines or have installed disabled it.