In the case of the specific question you flagged, yes, even moderators cannot migrate something over 60 days old, but that question wouldn't have been migrated in any case. You had cross-posted this same question already on Super User, so rather than add a duplicate to the target site, it's standard procedure to close the local one as being off topic.
As for the downvote, when a question is closed as being off topic, it is automatically downvoted by the system. This isn't something we control, so the moderator involved didn't explicitly downvote your question.
You can flag any question for deletion at any time with a custom flag, but please be detailed as to why you believe it should be deleted. If there's any redeeming value at all to a question (good question, good answers, etc.), we're most likely going to let the question stay. In this case, you could have flagged that this had already been cross-posted to Super User and no longer belonged here, and we'd probably have deleted it.
I've gone ahead and removed the question for you.