Thanks everyone for the thoughtful comments!
I can confidently say that apart from this occasional issue, this setup works well and my bootup times are acceptable (<30 seconds). I thought hard about using NVMe for /boot and GRUB but I wanted to separate out the /home drive because it’s easier to manage that way from a backup and upgrade standpoint. At the time I set this up, I had also read that GRUB and Linux in general struggles sometimes to boot directly from NVMe, although that might no longer be true (if it ever was). It would be a significant amount of work but I could potentially change this if we can demonstrate that there’s not another workaround, but I’m pretty happy with the setup overall.
@mladen I will get back to you ASAP — I’m at work right now but I can let you know when I get back home. I used the script MrChromebox uploaded here in August 2019 in case that information is helpful in the meantime.
@kieran That’s a good point. I’ll go through old kernels and see if I can reproduce it. I think that at some point GRUB or something else resolves it, but it happens regularly enough that I’m sure it will come back. I’ll try tonight! Unfortunately once it resolves it seems to stop happening for that kernel version. However, I might be able to reinstall a kernel that I had a problem with before and see if I can make it happen that way.
Any other thoughts on how to go about the troubleshooting process? At the moment I’m not sure what the next steps should be. I’ll definitely provide the information above as soon as I can.