There's always going to be, subjectively, a lot of overlap between those two categories in looking at the comments of others.
I know I'm not a troll, so obviously if someone downvotes me it's because they disagree and therefore unfair. But maybe not from their perspective.
You can also downvote and reply; I don't know how common that is. But given the number of people who say they don't know why they are downvoted, it seems to me like a reasonable thing to do.
Yes. "Look at this cool thing MS/Google is doing!" and "Look at this evil thing MS/Google is doing!" can both be seen as trolly agenda comments and relevant ones, depending on where you stand.
Would be cool if "downvote"(for relevance)and "disagree" would be mutually exclusive (either/or).
You either decide this post is not relevant to the discussion at all or you disagree with the argument.
"Upvote" for relevance and "disagree" could be combined.
You decide this post is relevant to the discussion but you disagree with the argument.
Of course everything depends on users using the tools in good faith. But it would be an interesting approach to decouple "downvoting" from "disagreement".
Downvotes are good for BAD COMMENTS. Things which do not add constructively to a discussion.
If someone DISAGREES however, that is what a reply beneath stating the disagreement is for.