This is a great topic and I have been trying to do as much research as I can on it before I post a full video dedicated to the ins and outs of content ID. (And more specifically how producers can implement it into their beat selling business)
I know that there are a few different ways to go about it.
You can submit your beats to AdRev or BeatStars and they will collect all your YouTube earnings from other people using your beats and monetizing their videos, however they take something like 20-30% commission from your content ID earnings. They then pay you out monthly or quarterly. This is what a lot of producers are doing already. Just remember, when you collect money from artists using your beats, they may be confused and be under the impression that they can make money from their youtube videos with your beats.
I also think that if you have a big enough business or youtube channel then you can go directly through youtube to use content ID. But I have also heard of a bunch of people being turned down when they apply using the link that you mentioned.
I think that this is still something new and people are figuring it out, I will try to make a complete video about it soon and help clarify what it the best way to go about everything.