Like the thought ... if anyone had such a thing would imagine Moodle Partner's would but doubt they would share such a tool.
All the things you've mentioned ... backups, for example, may not have one size fits all. My sandbox sites could be done with a single bu bash shell script, but the biggy ISD site has a 2 TB moodledata ... which, IMHO, is best done via rsync progressive.
Moodle version update/upgrade, as you already know, handled by a couple of bash shell scripts using git. Plugins ... only if those had a git repo of their own and probably work best if doing plugins same time one did updates or upgrades via git.
Security ... wow ... again ... one size may not fit all ... CloudFlare ain't a WAF (like mod_security) Then there are other things like mod_evasive.
Maintenance of DB server(s) and the DB's for each site involved - another one size doesn't fit all. Tuner runs on my BIGGY mentioned finds tables that need optimizing about once a month.
Then, also, would be nice to make that tool universal ... meaning runs on Linux as well as Windows and Mac's.
My 2 cents!
'SoS', Ken