I think you are confused by the following statement:
Don’t install the VMM management server, or other System Center components other than agents, on servers running Hyper-V.
However, that means that you should not run System Center components alongside Hyper-V at the physical server level. Running almost everything inside a virtual machine is recommended nowadays, and SCVMM is no different in this regard.
I would also highly recommend using Windows Server Core for the virtual machine that will be running your SCVMM instance https://www.starwindsoftware.com/blog/install-scvmm-2016-on-windows-server-2016-server-core. According to my experience such configuration is much more reliable and performant and requires less patching.
Good luck with your project!