Which Yocto build are you using? The latest Hardknott meta layer from us includes patches that do enable the 3.3V regulators for mini-pcie and m.2 slots at boot.
I can confirm the 5.10.72-lts with SR additions does provide power on the M2_3V3 for the Hummingboard Mate carrier board.
However, is there a table or list of SOMs that will provide the Mini-PCIe functionality when paired with the Hummingboard Mate?
For instance, in comparing the SOM B2B pinout for the iMX8M-Plus against the Hummingboard Mate schematic, it looks like the LVDSO pins are routed to the Mini-PCIe slot. Although, I’m happy to be wrong as we would definitely like to use the iMX8M-Plus SOM + Mate carrier board combination.
The main label of the pin in the SOM schematics is the default configuration of the PIN. The next label out is the alternate function of the pin used on our boards. However by default the Mate is a minimal board and does not bring PCIe functionality out to the mini-PCIe slot. There is an assembly option that allows this to work with the iMX8MP. You can contact our sales department to find out more details.