How to manage company Macs? What is the "Apple" way of managing Macs in company environment? I've red about macOS server and Apple Remote Desktop which seems to share some management features. The later seems a bit dated, at least judging by it's website that didn't receive revamp like the rest of apple.com pages.

What I need is


ability to manage software updates
some network config like VPN
Active Directory config (yes it's mainly windows environment)
e-mail is provided by company's Exchange server


And what about apple ids? Is there any option to have company controlled apple ids? We don't want private apple id's flying around ;)
macOS Server and Apple Remote Desktop (ARD) are just two of the tools used to administer Apple computers in or organization.

You could use macOS Server to sync up with Active Directory, but in my experience, you can simply join each machine directly to your AD server without the intermediary (in other words....it's not required)

As for ARD....YYMV, but personally, I would rather use custom scripts to push out applications and updates

Apple has an excellent service called Apple Deployment Programs which helps you manage everything from AppleIDs to macOS and iOS deployments.  Contact your Apple business rep to help you set up this and your AppleIDs specific to your organization.