What works for me is file naming. It has to contain the subject, the source and the priority “AAA.Zettlekasten method - Linking strong.Site xyg”. No tag, nothing. I read, I keep or note and I suppress the article. Everything in the “Read it later” folder is meant to be read and destroy. That’s a todo list by itself 
Yeap I read it on Obsidian. Much smoother to my eyes, to begin with and allow me to transform a reading into an zettle right away. The import folder is a temporary one. Extract something to a source is to work on it and transform it so the file don’t stay “as it” for long.
While reading, I create one Note per citation/ideas, and a main note to present the article and the source in my Litterature Note with every Notes linked to it.
I work with a side by side view just like this :
The left one is the main article, the right one is a temporary litterature note. I have already put my templates of note into it and begin to take my note. The blue lines are my own questions to further research.
I work almost the same with PDF : I put my reader to the left, and write to the right. I rewrite everything and copy-paste quotes direct in my markdown notes, their is nothing left of the initial extract (poor thing ahah).
If I want to keep some parts (for example I really like to cite Homer, Ovide or Pratchett), I cut and create a new document in Obsidian for individual citations and link it into a Litterature Note.
"# Homer
Note :
(Littérature Note here)
Citation
- [[Homer.Illyade.Chant 1.Trucmuche]]
- [[Homer.Odyssée.Chant4.Machinchose]]"
And so on.
I hope it can help you to create your own system
The less is the best from my point of view. I relate to your feeling very well and it took time to find something that works for me. I hope you’ll find it quicker than me 