Hi aethereon,
The main difference is regarding what you plan to do with it, here's some cases.
-for smoalking you should use the freebase.
-for oral ingestion it doesn't matter much, the stomach acid will convert it to a salt form anyway.
-for sublingual both would work but the salt form is very bitter while the freebase is nearly tastless.
-for long term storage the salt form is more stable, freebase harmalas can turn into the mysterious haramala red.
-for accurate dosing the freebase is better as the manske produced salt might be contaminated with salt (NaCl).
Regarding the washing, it's meant for the freebase and it as simple as topping the container with water, waiting for the freebase to settle and decaning the water. Harmala salts are soluble so they cannot be washed with water.
When acidifying a lye solution, the NaOH is turned into a sodium salt + water, and it will stay in solution when you produce and collect the harmala salt, there might be trace amounts trapped in the water that the filter absorbs but nothing to worry about. In any case, dilute NaOH is not harmful and is used in food products.
You should worry about NaOH when you want to produce the freebase. To deal with it, first thing is to not use excessive amounts of NaOH, and then doing water washes to make sure the NaOH is diluted to the point where no harmful amounts are left when drying the freebase, and remove as much as possible of the water before drying the freebase. You can also do the final basification with sodium carbonate mainly and only use a few drops of NaOH to drive the PH higher so the solution is no longer yellow, followed by water washes.
The trick to an easier harmala extraction is to directly basify the rue tea before any filtration, and then do multiple water/base washes and decanting, this will get rid of most of the sludge that makes harmalas hard to filter. You can then do a crude manske step. After that you can continue the way you want and filter the solution during an acid step to get rid of any undisolved material.
making the rue tea with whole seeds is also less messy and reduces the sludge and other contaminants.