Hi James,
These differences are being actively worked on James. Although as you noted there are some key areas of difference that are not easy to upstream as they currently are.
I believe two key areas you may run into is lack of cros_ec support for updating the EC and lack of a ignore_error feature in the cros tree for dealing with the ME.
We would like to replace both of these mechanisms with a cleaner upstream one however the effort needs to be resourced.
What was your specific problem?
Kind regards,
Edward.