The problem is time.

While it is true that in groups of 2-3 people the ambush ninja can be cleared without much trouble, it will take probably 3-6 minutes to kill one of those teams.

Now in a non merged server where there are 3-4 people capable of beating the ambush ninjas due to lvl differenceor many other factors, if one of the is missing, your strong members effectively loose half the alloted time to kill the summon. Not only that, but the weaker players that heped kill the summon have to wait for al ambush to be cleared.

In a non merged server, that means that a sizable portion of your main damage force is wasting time with ambush ninjas and by the time they finish, they do not have nough time left to do 10 rounds against the world boss.

In theory if you could kill the summon before you can still kill it now. In practice, if you have few members (say around 6) that participate in summon capture and not everyone is strong enough to beat in pairs the ambush ninjas, then you will not be able to kill the summon. Specially since not all people can be there at the beginning of the summon capture.

It's not all about strategy and whatnot in a time limited event. While it's more fun imo this way, its true that in our server none of the 2 active groups has been able to kill the summon yet. It's a fact that killing it is much harder now.