Hi TECMike,
Thanks for the good words.
I too have a lot of eternabond up there. Every Dicor'ed anything that was a primary water seal was Ebonded over starting back in 2010.
Here is my roof after being washed 2 summers ago. This is a 16 year camper. I washed it 4 times a year when it lived outside all the time until 2013 when the new barn came. Now 2 times a year being stored inside. And I put 303 UV protectent on everything up there after washing it. The 303 for sure helped.

To your question about only coating the areas that are not eternabonded, when mine comes time to be coated, I was looking heavily into the high solids silicone treatment. The Henry's or the Crazy Seal. They will cost more then the other coatings, but this all comes down to how much longer does one want to keep the camper? Do you need a 50 year warranty?
In my case, it could be another 16 years or more. I may get a new one sometime or a different one, but I do not think I will ever get rid of this one. Like yours, everything in it is dry and in top maintained shape. I sealed every siding joint too. Trust me I spent $$$ maintaining it.
When I installed the Ebond, I put a light coat of non sag Dicor caulk on the exposed sealant edge of the E bond. This flowed over about 1/8" to 1/4" onto the Ebond. I did this to not have dirt stick the exposed E bond layer. I'm not sure what you did.
When I coat the roof, I will coat over that Dicor and stop there just past the Dicor. That is due to the coatings I am looking at. Since I 303 the Ebond, there is no notable degradation on the white layer of the Ebond. Since I still need to treat all the roof plastic up there, this would not be an extra step, just do it when I treat the rest of the plastic.
The folks with the Heng's, for me that is an unknown. I have no data to prove it is a problem other then the issues I have found on other brands of acrylic coatings. If the coating did lift off the Ebond, as long as it did not tear into the main roof coating, it may not be an issue. If it would make a clean break and stick solid at the end of the Ebond and not cross it, well you can see it and then figure out what to to.
You could also coat up to the Ebond from the start and not go onto it. If your Ebond has no signs of top layer degradation, that at least helps give you part of an answer. From what I know, if the top of Ebond is UV treated frequently, at least 2 times a year, more is better, the Ebond may last as long as the camper will.
Hope this helps.
John