YouTube has a new trend, "This video has not been made available to mobile by the publisher."
Playing around with it, as a "publisher", I see no way to set that level of granularity. I think YouTube/Google is making those choices and deflecting the backlash by making it look like the "publisher" did it.
On older Apple devices/versions of iOS, it seems that the error message is the one you've seen more often than the new one.
I've even seen one video that refused to play if launched one way, but would via another.
I suspect that YouTube is not transcoding all videos to all formats anymore by some metrics of how many views something has had, or similar.
I suspect also that this is rooted in not having enough disk space and CPU to transcode and store them all. Cost cutting. Nothing free lasts forever, and the mobile device players often don't show the advertising which is typically paying for the service.
I can't say that I've gone hunting very hard for all the answers as to why various videos aren't available in all formats, though. I'm sure it's a mix of all of the above.