It is not broken. You can use In to hide your Nen which happens a lot in fights in HxH.
The small detail i was talking about is that you claimed that it makes no sense that In is an applicatin of Zetsu (which totally makes sense), and this is a small detail you are nitpicking on ground of nothing at all.
The usage of In, Gyo, Zetsu and ryu was consistent throughout the whole manga since those concepts were introduced.
When Nen was introduced by Wing, he explained it (being a martial arts practioner) in a way which is common in martial arts.
It enables you to easily understand what to do to accomplish a certain thing.
In Karate for examples (at least in some styles) there are animal analogies for certain techniques so you know which mindset you should have when you use one of those techniques, to make you understand what your body should do when executing that technique.
It is the same here, it is obvious that to hide your nen you have to be able to control you nen flow, aka using zetsu to stop it but not completely stop it.
Thus In is a technique which is harder to pull off than zetsu, but being able to use zetsu is a requirement, thus it is called an applicatin of zetsu much like a technique in karate might be called a techique out of the tiger style though you are 'spoilers' not really turning into a tiger to execute it.
It is not hard to understand.
it is also no flaw.
It is not even badly explained. It does not contradict anything, it is consistent throughout the manga, i really do not see the problem.