Patching and rebooting
Patching is a centralised operation. It's significantly easier in a virtualised environment because I have one application per operating system. I have to test if that patch on that OS affects that application. I have no weird interactions between all these different applications in to debug. One app per OS. Test and release centrally. That part is easy as pie.
Now, rebooting is again made easier by "one app per OS." Rebooting the OS reboots the infrastructure under ONE application. Just one! I don't tank the whole business with a single reboot, I don't have to schedule reboots around 15 different departments. I call up the people who use that application in question go "hey guys, I need to reboot the server for updates, mind if I do that tonight at 7:00pm?"
I get a yay/nay and move forward.
I can schedule and co-ordinate each application independently of the others, and that is a bloody GODSEND. You see, I work in a business where IT doesn't have the almighty word of God. We don't dictate when computers will be available. We work with the affected business units to ensure the best possible quality of service with the fewest possible interruptions.
That means worrying about things like downtime. It also has to bear in mind the real world, where we have telecommuting workers in the systems 24/7.
I can not even conceive what it would take to coordinate a shutdown of the entire corporate infrastructure at any of the companies I oversee. A miracle perhaps. Or 6 months worth of proactive planning.
Virtualised and containerised environments make patching/rebooting EASIER. Yes there are more widgets to reboot, but you can do it without nearly as much angst or worry.
As to tracking and monitoring and securing a fleet of Windows servers, have you tried combinations of some or all of the following:
Active Directory
Novell Zenworks
Windows Server Update Services
Windows InTune
Microsoft System Center Suite
Nagios
Spiceworks
Puppet
++squillions of others
If managing a fleet of servers - physical, virtual or otherwise - to know "are they up, are they patched, are they infected - is a difficult chore for you, then you are doing it wrong. It's easy to do...and there are programs that let you do it for free.
Managing computers is EASY. Managing people (and budgets) is hard.