UdoG

Yes they are. You should install them for proper system function. 

Well it’s not a firmware issue. It’s because those ports are provided by third party controllers, Genesys for USB2.0 and Asmedia for USB3.0. So they are not initialized before OS. You can change the settings in BIOS to initialize them during boot but it will make your POST time longer. 

M.2_2 should be working with Comet lake. M.2_3 and M.2_4 are PCH attached slots. 
 
It could be a PCI-E allocation issue as USB controllers are wired to the PCH, not the CPU. For 11th gen, the bus between CPU and PCH would be DMI x8 while it's DMI x4 on 10th gen. That might be the reason for it but I have to verify that myself. 

The fine tuning has occurred...minus the cables. I ordered sleeping to bundle the front io into on clean loom but it hasn’t come in yet. I swapped the color of the vue coolant to a redder color and corrected the angles of some of the runs so it’s all straight.