https://github.com/X16Community/x16-docs/blob/master/X16%20Reference%20-%20Appendix%20F%20-%2065C816%20Processor.md#compatibility-with-the-65c02
According to the images here the 65816 isn't cycle compatible with the 65c02 when reading registers with side effects.
These are worth mentioning as they could cause subtle compatibility bugs, not just with the vera data ports, but any IO device.
I've not been able to check, but I assume the undefined 'nops' are also different. These are also useful, eg having a 1 cycle nop vs the documented 2 cycle version.