Yeah, I was wondering myself, a while back. I knew they weren't canon, but the Meryl just leaving explanation seemed a good one to me, if she stayed with Snake after Shadow Moses, then this would be just the way she'd leave, in my opinion.
Yeah though, I worked out they weren't canon for myself, or pretty much everything in that Tale wouldn't have fit into the Main story.
The non-canon ending with Otacon too in MGS1, Campbell says Meryl was his daughter, but there you go, it's all non-canon.
I personally think Kojima could have explained a bit more about it in MGS2, possibly during chats with Otacon.
Oh, and if anyone ever gets the irresistible urge to play this tale or any others, check us out
Here.
You're all welcome with us. :lol: