I don't it'll ever be a problem given how long the transit is.. they're probably going for the safe side. Also given the small operations they have at Miyazaki, perhaps there is a chance they are not used to seeing layovers this long? Thus are confused about the possibility of leaving the transit area? There's always a possibility i guess...
Also I'm also assuming (with the others) that this is on HX? CX/KA doesn't fly to Miyazaki.