Welcome!
"If I select to backup also users and groups, these users will be created / overwritten in the new moodle instance?"
That's one of the catch 22's using this method ... yes, users included in the backup will be created - not overwritten.
But, if an admin level user has been made a teacher in a course on original server and you restore to new server, potential snafu with role conflicts.
And, authentication needs to be setup same way before restore of course.
Comment: depending upon the number of courses, this method will really be the one with the most work.
A site migration brings everything across, but one might have to dummy down version of PHP (package manager of OS) before the 3.11 code can run. And one needs to check out MySQL/MariaDB version as well.
Once the 3.11 up and running one could get the code under git versioning and that, by far, is the best way to update current code and upgrade to next Moodle version upwards.
If you use git, you won't be in the situation you are in now! . And it's really easier to maintain the version you are running. Considering that moodle releases updates to code every week.
'SoS', Ken