I would suggest to not filter rue tea at all, such step is not needed and is very annoying.
You can directly base tea still with some sediment in it if you want, it does not matter much.
First filtering is necessary only after dissolving precipitated freebase again in acidic water.

I agree that sedimentation/decanting method is great and should be preffered over filtering.

But it's common in plant extractions that after concentration of some plant "tea" a sediment forms despite the tea was filtered before. Solubility of various compounds and their mixes is very complex, quite unexpected behaviour often occurs.

A possible sneaky trick when redissolving freebase into acid/vinegar is to put the powder in a funnel sat on top of a wad of cotton wool and slowly trickle the vinegar/acid through it. A dropping funnel would be ideal for this slow-dripping of acid onto the harmala base but it's not essential. This should clear up a certain amount of the annoying particulates without it being as much of a pain as filtering an actual harmala solution, which is often a complete pita nightmare.

I wonder why use acid at all when one can just boil harmala seeds in water and obtain the same decoction. I've tried that, and it worked well for extraction, just like for rue tea.
Could you please elaborate?
Thanks!