I have a 5 second DISARM_DELAY set, and have observed this behavior with autonomous flights when an automatic landing is performed.
In my opinion, this is not a problem, and is instead an important feature of operational safety. The airplane will not allow itself to be rearmed until the operator intentionally and specifically resets the mission. Otherwise, it would be possible for the aircraft to land in AUTO mode and an unintentional arming would send it on it’s way again (also assuming you wanted the mission to reset). The current two-step process requires an intentional action from the operator before you can fly again in AUTO mode. That’s a good thing, and I encourage everyone flying in AUTO mode to view this as a safety interlock feature and not an annoyance.