I did find one thing which is interesting, which is that if I boot into the first kernel with xencons_poll, and the second kernel without it, then the console in both kernels works. I wonder if perhaps the first kernel needs to unhook something irq related.

For completeness I tested all the combinations of booting with and without xencons_poll

First Kernel Second Kernel - - No input on serial console - xencons_poll Success xencons_poll - Success xencons_poll xencons_poll Success