The original problem that we had 209345 was that we could not turn the SPI on using JetsonIO. That was a bug. After some considerable time looking at this we discovered that it was because the boot procedure was not properly checking all the available boot options in the boot-order and was giving up at nvme when one was present. Having remedied (ie not fixed) that by changing the boot order, the next machine we tried to set up we could no longer boot with our custom dtb that was turning SPI on and after some more considerable time we discovered that it was because extlinux.conf was not not being read and thus found this thread.
So I am inclined to agree with user100090 that these are all related and part of the same issue. Recompiling cboot is clearly raising more bugs and I am not inclined to try it and will rather stick with 32.7.1 and change to boot-order.
So when will the combined boot-order + extlinux.conf bugs be fixed?