Some development here,
I noticed today that while applying Dan's patch and reverting the "bad" commit resolves the issue, it only does so on a reboot. The boot is still slow on a cold boot. As you said this might very well be a mix of different issues. It is my own fault for not reporting this regression earlier thinking it would be fixed.
As a sanity check I retested old LTS releases. I find that v6.1 does not have the issue on cold boot while v6.6 does. The USB error messages are there regardless, they just don't impede on the boot process time. I am almost 90% positive that those error messages have always been present on this system, for what it's worth. I have gone through the troubleshooting step of unplugging all USB devices and headers and the errors are still present.
If I find the time I might run another bisect between v6.1 and v6.6 doing cold boots instead of reboots and report back. I am just afraid I will just get back to the initial commit reported since this is what I first did.
Thank you.