Pretty sure it's the "youtu.be" vs "youtube.com" format that determines what gets loaded into the archive. The former is what appears when a user clicks the "Share" icon on a YouTube page and copies the link that appears below that. They both link to the same vid (see here), but presumably MM has written the code so that a vid is only loaded into the archive when the "youtube.com" format is used.
I actually like having the ability to post some YouTube links that won't get put into the archive, especially ones that are an hour long but have like two minutes of mess in them (lot of wasted server space if archived). That's when the "youtu.be/{videoid}?t=XXmXXs" format really comes in handy. And there have been many non-messy humorous, instructional, music or other referential vids that made sense being in a messy thread. Still a few quirks in the system (like some links coming up un-clickable) but I like it the way it is.