Once a show, or an episode for that matter. it will not appear on deck. The only way to get it back on deck is to, as you said, mark it unwatched.
It is just what it is and, even though you have a valid point about Trakt.
I cannot conceive any way to get the behavior you want as on deck is specifically designed to show the next unwatched episode after the last watched one.
Personally I like the way it behaves now and I would not want Plex to attempt any dubious improvements. In fact the only change to on deck I would like to see is that if there is a watched episode after some unwatched ones I would like the actual first unwatched episode to show on deck instead of the first unwatched after the last watched. But I am reasonably content with the way on deck works now.
Surely something could be developed to support rewatching series and you liking or don’t liking whatever there is implemented right now is not the point. Point is that rewatching tv show if you are using trakt is pain.
At some point (hopefully) Plex will finally introduce native support for trakt and simply marking as unwatched won’t cut it.