I think the main role of the "Manually sort folders" add-on for Mozilla Thunderbird has been moved to the core, but there is one more thing left to do.
It is to select a specific folder on startup.
I suppose there is a way to create a new add-on for this without modifying the core, but there is no guarantee that it will always work with a monkey patch. Maybe the WebExtension API would need to be extended, but it seems silly to do that just for this purpose. Then I came to the conclusion that it would be better to deal with this by changing the core.
I have started a discussion about this in the 'Thunderbird Developers' chat.