When you add the lye in step 5, that gives you freebase alkaloids that are not soluble in water. That's why you're waiting for them to settle to the bottom, so you can decant the lye liquid off the top.
Once you've decanted (removed) the basic water (high ph water) your goodies are still at the bottom of the jar.
When you add vinegar and hot water to these alkaloids, they will become harmala acetates which is a salt form. When the alkaloids are in salt form, they are water soluble. So this means that they are in the solution and can be filtered. When you filter this solution, anything that gets left behind in the filter is unwanted plant material.
When you proceed to step 6, the manske, that will convert the alkaloids from harmala acetates to harmala hcl which is a different kind of harmala salt.
You alkaloids won't be freebase again until step 11.
Hope this helps and welcome to the Nexus.

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