Internet Explorer 11 has an integrated Adobe Flash Player plugin, but on Windows Server 2016, this plugin is not active by default. In fact, checking the available plugins within IE does not show the plugin as installed. This is because the plugin is not activated by default (which is somewhat logic as it's considered a security risk).

The package containing the plugin does exist on Windows Server 2016 (with GUI) but is not active. You can manually activate the plugin through dism:

dism /online /add-package /packagepath:"C:\Windows\servicing\Packages\Adobe-Flash-For-Windows-Package~31bf3856ad364e35~amd64~~10.0.14393.0.mum"

After adding the package, you will have to reboot for it to be available within IE.