I honesty don't think you're actually doing anything particularly wrong. In a way, your queries kind of remind me of another member, Chasly from the UK: loads of interesting questions, with so very many of them inexplicably downvoted, or closed or reopened or closed again or argued over. Bizarre.
You've been at SE long enough to know the basic rules. You're kind of new to WB.SE, though, and it could be you're not quite up to speed on how they apply in this forum.
I certainly don't think you're doing everything wrong, but there are two main issues I've seen with your questions:
- you like to write, so you do have to be careful when approaching the ill-defined marches of what we consider to be "story based" questions (I think your extinction level query and perhaps even your binary virus query can be argued as being story or plot based.)
- take care to read, reread, edit and reedit your queries so that they all ask a single, focused worldbuilding question for which we'll provide you a single, focused answer. You also say that you tend to overthink. This often results in "overwritten queries" --- too many nebulous ideas, too many possibilities. Generally speaking, when title and body don't match or when an OP asks multiple questions or suggests multiple variations on a theme, we tend to mark the query as too broad. You are cèrtainly welcome to ask multiple questions! Just ask them one at a time (and for preference, append links to related questions).
As for writing questions "correctly" ... the strictures are really imposed by Stack Exchange itself. The model being one single, focused query gets one single, focused response. But our art / activity / hobby is not like physics or math or history where discrete questions and answers are possible. Almost every question here is, in some way, "opinion based" and "broad".
Generally speaking, less is best when it comes to queries. If someone writes a comment to the effect of "so basically, can XYZ do DEF", chances are good you overwrote your question in the first place. Maybe too many details, maybe too many directorial orders ("good answers will tell me..."), maybe too many nuances.
I honestly don't get all the downvoting, though. I've not downvoted any of your queries (that I'm aware of) and have upvoted several recently. Just my opinion, but downvoting should be reserved for poorly written, poorly researched, inappropriate questions. Otherwise, vote to close.
For the linked query under consideration, the virus one, I note that you got a number of excellent and thorough answers. While I'd consider the question to be arguably "story based" (you're asking about a plot element), I see no reason to downvote it.