I know this is marked as solved, but I wanted to chime in with another potential solution.
I was having the same issue, certain USB ports not working, WiFi & Bluetooth not working, etc. Went down the rabbit hole of BIOS settings and ended up here. pci=nommconf did solve the issue, but it was really bothering me and I knew there was something weird going on with the PCIe bus that was causing the issue in the first place - so I started disabling as much as I could.
Turns out, it was a super simple solution - just took forever to figure out. Flip the physical VGA switch to off. That solved all the issues I was having and I no longer need the kernel flags in GRUB. USB Ports, Wifi & Bluetooth are all working with no more dmesg errors.
When I first built my machine, I used the onboard VGA adapter to connect to a monitor in order to install Ubuntu. Once I got Ubuntu installed, I installed my GPU, and I changed the BIOS setting Boot → Boot Configuration → Primary Display from Onboard VGA Header to Discrete graphics card. Turns out, this does not actually disable the onboard VGA header - so I’m assuming it was causing issues for other PCIe devices. In order to completely disable the onboard VGA, you need to flip the physical switch to off.
If you have a discrete GPU, you shouldn’t need the motherboard’s VGA anyway. The switch is located in the bottom right portion of the motherboard right above the VGA header.
Hope this helps.