When rebooting sometimes restarts without onboard audio available
I haven't observed the lack of onboard audio on reboots, but I usually don't reboot my Blackbird much when it's on. On the other hand, I still occasionally have situations where it won't put video up on HDMI, or at least my home projector won't see it.
VLC sometimes remains "running" after closing out
This is not specific to the Blackbird; I've seen this on the Talos. I haven't figured out why this occurs. A killall -9 will nuke it.
Alternatively, go to the settings and uncheck Allow only one instance. This doesn't solve the problem but it makes it much less annoying, and you can clean up the corpses later.
Large images in GIMP are much slower to work with
I haven't been happy with GIMP on
any platform. I use Krita or azpainter.
Some of your other issues sound more software-motivated, but I think that PCIe-NVMe bridge might be a little rickety.