You have the reputation required to vote to close questions as off topic or to have them migrated to a different site. When you flag to have something migrated, you're using the tools you're given the wrong way.
Whether a question is on topic on this site is completely independent of its quality. The question you linked to is, IMO, not low quality. Low quality means:
This question has severe formatting or content problems. This question is unlikely to be salvageable through editing, and might need to be removed.
None of this is the case. The question's formatting is very good, and its content is substantial and easy to understand. It's not on topic on this site, correct, but your flag was still wrong.
The most important thing to keep in mind is the following: You flag to help the moderators keep order on the site. In the flag reason, you tell them why you flag a question. In many cases, I use the free-text input field to explain it in more detail.
As you can imagine, the handful of moderators we have often need to deal with many flags. In some extreme cases, they're simply overwhelmed. This is probably very rare, but still. The point of flagging is not to increase your flag weight, but to help moderators keep the site clean.
Once you've used the site for a while, and by participating and contributing have shown you know how the site "works", you get additional privileges. The relevant privilege here is vote to close. The site owners trust you to know what is an appropriate topic on the site, and what isn't, and with a few other users, you can close topics without moderator involvement. This helps keep their workload down.
That's why, starting with 3000, you don't flag as e.g. off topic, but vote to close. When you view the flag dialog, you'll notice
"This question does not belong here".
This is what you should have clicked all along, and it will open the vote to close dialog instead:
Now, below 3000 reputation, it looks like the following (screenshot from a different Stack Exchange site where I have 300 or so reputation):
Under no circumstances do you need to flag as "very low quality". If the question doesn't belong, there's a list item for it. Below 3000 reputation, it will result in a flag. Above it, in a vote.
"very low quality", you simply aren't helping. You have the privilege, through your reputation level, to vote to close and should have started using it a long time ago. Yet you continue to flag instead, for a wrong reason which requires moderators to do what you should have been doing, which is voting to close, and requires them to decipher the flag message: Since the question is not very low quality, your flag doesn't make sense. And that's why your flag was rejected.