Correction, this is only the case for the official worlds, not all read-only worlds - so likely just a part of your publishing process.
While it would still be useful to preserve these layers (both as reference material and for making derivative content), this is not actually a technical issue and can be closed.

Thanks!
Do you know if this will be supported in the future, or not at all?

With "potentially log the specified addonList" I just meant the message printed in GetGame().PlayGameConfig(), a function which calls RequestScenarioChangeTransition().
It's not actually relevant to the problem other than that it confirms I did not just accidentally give it the wrong input. Apart from that, nothing is logged either way.
But here's some detailed info on how to replicate the problem:

Any updates on this?