Although I've read all of the messages in it, this thread has not been especially easy to follow.
Whatever changes are made, we should ensure that there are no regressions as a result. This should mean that: 1. Existing Org users who install the new version of Org and export documents to HTML should not see any changes in the output. 2. New Org users whose first version is the new one should be able to easily get the same HTML output they see existing users getting. If the changes in documentation and in-Emacs messages obscure the necessary steps, it should be considered a significant regression in usability. I can already imagine the messages asking, "How do I get the nice-looking, syntax-highlighted code blocks I see all the other Org users getting?" There are already many questions about Org that are asked over and over again in various places. Let's not add a new one to that list, about something that used to work fine.