This is a common feature. The only boards that probably won't offer this are going to be your lower end budget oriented models. The aforementioned GIGABYTE B450 mITX isn't one I have experience with, but I believe it.
Rather than worrying about disabling SATA/NVME ports have you considered virtualization? You could run a hypervisor (VMware ESXi, XCP-ng, Proxmox, etc...) and boot as many different OS as you want and isolate resources. Better yet you can run multiple OS simultaneously with as little or as much isolation/separation as you want. You can even do direct passthrough on some things, like run a Windows VM and passthrough a video card so you get optimal performance or access to hardware resources you want.