I highlight as a way to categorize my annotations. I highlight in Zotero as I go, and in the highlight's comment section briefly jot down why (e.g. something to follow up on, or whether this reminded me of something else it contrasts with). I dedicate a certain colour to "background references I should have", another to ~ "things I disagree with" etc., which I find useful when coming back over the paper to type up my notes.
In a sense the highlighting is just a way to localize my thoughts to a particular passage of the text, and the colours (or even highlighting at all) are secondary.
There's some considerable duplication of effort (notes in Zotero, then I type up notes in Obsidian, then also extract out some of those ideas into their own files). But, much like the recent posts about "outsourcing thinking" and GP noting that people sometimes do nothing with their highlights, I find that the work is useful for understanding and remembering.
Out of interest, why have you been considering Logseq?