Directly changing a theme causes a "Functional environment bootstrapping" error
I wasn't inside the sites' folder! I didn't notice that for some reason - Here is a possible explanation why, that might be nice for you to read:

In the similar time period, I also ran a few general Drush commands inside the root folder just to check if Drush itself is working because of Environment Variable (Path) value setting mistakes I made earlier and tried to fix; I could run drush in each session only after manual var export, but I than went to home/.profile, and added export PATH="~/.composer/vendor/bin:$PATH" in the end of file and it fixed it.