What is the right place to ask about web applications' desktop software?
Super User or Web Applications spring to mind.
Stack Exchange seems like a good place to ask questions especially strictly like "what happens when you tick this option?".
No, not really.
We're not a tutorial site or a replacement for software companies that can't be bothered to document their stuff.
You're free to ask about the result of you ticking that self-destruct option and then ask about the disappointing result.
The problem is where to ask. As it's desktop software, it's against the rules of Web Applications, even though its purpose is to interact with a web application (both Google Drive and Google Photos).
Hmm. Based on a quick search both Super User and WebApps seem to take such questions. You can ask on the per-site meta if your question is on-topic. It is shown I'm not familiar with the scope Webapps as I just learned questions about that tool are off-topic there.
But as soon I tried to ask such a question on Super User, I was immediately encountered with hostile comments ("How about you do as instructed", which BTW, I did), got points dropped and had my question paused (one of the voters also wrote a comment that explained about Google's quota that had no relation to the question). It doesn't make me want to ask any more related questions there.
I don't see any hostile comments, to be honest or some must have been deleted. Don't mistake comments that are to the point for being hostile. You're free to not like that tone but please stop calling everything that doesn't come with an emoticon hostile. Asking "How about you do as instructed" was meant to invite you to provide more details to be added to your question. You answered in a comment. Make an edit to include that comment of yours in your question.
Is Stack Exchange just not a place to ask about web applications' desktop software, or is there a more fitting place than Web Applications and Super User?
It depends. Both sites could work, if the question doesn't sound too much hypothetical or explain how this works. For example your title could be
Why didn't the Google Backup & Sync desktop app honor the "Upload photos and videos to Google Photos”
and then explain in your question what you did expect that option to do and what it did instead. Maybe provide information on what made you think that option applied to your use case.