Declining flags isn't an entirely objective process, the rules are pretty fuzzy and there are many differences in how moderators handle this. There are also some issues with the tools and the flagging process in general that lead to situations where reasonable flags are sometimes declined. Most users, including many moderators, are also not familiar with all the details of the whole flagging system. They are not documented well and have changed signficantly over time.
Declining flags is also not meant as negative as it is often perceived. The main purpose is to educate user on how to flag more effectively.
The big principle of flagging that was already mentioned is that you shouldn't use flags for issues that you can address yourself and that don't need moderator intervention. If a question should be closed, use a close flag or close vote as those are handled by the review queues.
Now, regarding the specific flags mentioned in your post and WYSIWYG's post:
The flag about migration to Physics is a reasonable flag in my opinion. Migration is something the community can't do, so involving a moderator makes sense. But I can see declining the flag if the moderator considers this question to be either too poor to migrate, or not off-topic at all on our site. I would probably have validated the flag, but not migrated this post if I had handled it. But I can easily see myself declining flags in rather similar circumstances. The question was self-deleted by the author minutes after your comment and flag, so this isn't any evidence that it was off-topic here.
Regarding flag 1, I would have declined this one as well. You should have downvoted and/or flagged to close the question, there is no need for a moderator flag in this case.
Regarding flag 2, this isn't really VLQ in my opinion. Closing it because of the vagueness of the question is probably justified, but again no reason for a moderator flag.
Regarding flag 3, there was no reason to act on that question in my opinion. Even if the user was a creationist, the question wasn't really problematic. And the comments were unnecessarily hostile, I removed them in the meantime.
Regarding flag 4, I can't argue that this isn't VLQ, it clearly is. I generally prefer using close flags on questions instead of VLQ, I don't think the VLQ flag should even be available on questions. But as my own opinion here differs from the guidance on the flagging dialog, I would not decline such flags in cases of truly VLQ posts.