If you have a Castle in slot 1 with 3 Crystal Towers than switch to slot 2 or 3 merge the three crystal Towers and than go back to slot 1 you can place the tier II Tower but also keep the three Tier I Towers
This way you cannot dupe the towers because you have x-3 Crystal Towers but you are able to place more towers than you should be able to
Like you said it doesn’t enable to dupe so it’s not huge issue. Plus eventually you will want to make changes to the castle anyways atleast this way you have a fall back if you regert your merge (just use the other slot until you gained back to do changes)