I also have in Waterfox on macOS: extensions.e10sBlockedByAddons=true (modified) extensions.e10sMultiBlockedByAddons=true (modified) I had set these to false in my profile on Firefox 56, before moving the profile to Waterfox. I never changed them manually. I'm not sure when or how they were changed.
But multiprocess is still "Enabled by user", even though I have addons marked "incompatible" (which actually work fine). So, it is not important. I don't want multiprocess to be automatically blocked by incompatible addons, and it isn't, even with those prefs true. So that's ok with me. But it doesn't seem quite correct, if someone actually wanted that behaviour, they wouldn't get it.
--NRG-- you said "I never had issues with enabling multiprocess", and the prefs "cameback to TRUE (multiprocess continued to be setted enabled)". If multiprocess is not blocked, then what is your actual problem? Why not just ignore those prefs? Why is it important that they come back to being true?
I don't have the preference: browser.tabs.remote.force-enable and it doesn't seem necessary.
The preference: browser.tabs.remote.autostart is controlled by the "Enable multiprocess Waterfox" checkbox in Preferences. When it's checked, and the pref is true, multiprocess is enabled, even though extensions.e10sBlockedByAddons=true.
The preference: browser.tabs.remote.autostart.2 is partially controlled by the "Enable multiprocess Waterfox" checkbox in Preferences. It was true, then I unchecked the checkbox and it became false. But when I checked the checkbox again, it remained false. Multiprocess is still enabled though.