After running into the same issue and reading this thread, I opted for trying a different editor than the default TinyMCE
I installed “CKEditor for WordPress“, and while it doesn’t show the custom HTML properly in Visual mode, it does leave it untouched, so even if I (or anyone else) edit the post via Visual mode, all remains good as long as the custom code areas remain untouched.
+ The CKEditor feels a little better anyway (but keep in mind I only worked with it for a couple of hours so far).
DD – it seems you’ve enabled your scenarios already, but hopefully this will come in handy for the next person in line that goes through the same problem.
