Bowlfish assumes that after it boots, the single hard disc in a system will be wd0a. Not true on a Soekris net6501 when using a USB volume. It’s sd0a. You need to update /etc/fstab to mount / from sd0a instead of wd0a. You can do that with a site.tgz file, or just mount and edit the disc before you boot. Or mount -o rw,noatime /dev/sd0a /mnt on the booted system, make the change to /etc/fstab, and then mount -o rw /dev/sd0a.
Until you fix that, the ro and rw aliases won’t work, and any reference to the disc will get errors “mount_ffs: /dev/wd0a on /: Invalid argument” Changing /etc/fstab makes it all work right.
I used an etc/fstab file in my site.tgz, as I already had a site.tgz I was working with. I took the chance to bump up the size of my ramdisc while I was at it.