@CaseySJ
I have two TB3 external enclosures with SSD drives. One of the first things I did when I booted this B550 the very first time was to check how TB3 worked without flashing. I duplicated your findings and these TB3 drives showed up on hot plug and warm boot. (This was with Catalina 10.15.6, and OC 0.6.1)
TODAY after using the TB3 port to drive my TB2 display yesterday, and unplugging the display and using HDMI, neither of my TB3 external drives will mount! (I tried both Big Sur public beta, and Catalina with OC 0.6.2)
Thinking I may have messed up some OC settings, I went back to my very first OC 0.6.1 EFI backup with both Big Sur public beta, and Catalina and still no TB3 drive mounting.
I confirmed that TB is still enabled in BIOS. I confirmed my TB display still works so the ports are working. I attempted to reset CMOS by shorting the two pins on the board several times, but the board never acted like the reset had worked. I loaded the BIOS "Optimized Defaults" and tweaked them as needed. I also loaded my saved BIOS settings. I also flipped BIOS setting for TB to OFF, rebooted, then flipped the setting for TB back ON, and that didn't change anything.
I'll next remove the CMOS battery to see if that makes any difference.
Both TB3 drives mount on my Z390 Designare (Flashed) without problem, so they are working properly.
It's going to take more investigation to figure out why TB3 is currently not working with my external drives.
I don't think I'm dreaming about my initial success with the TB3 drives, because I was happy to find out I didn't need to flash the TB chip.