Yeah, all the fantastical elements in the MGS series always seemed to be there to enhance the story, not for autopsy by fans, Vamp for example, was supposed to be able to do ridiculous things ("He's running on water") in order to make you wonder what the hell was going on, not for you to explain why he was able to do it.
The La-Li-Lu-Le-Lo was supposed to be an "avatar" for the developers, since it's them who dictate the course of the fiction you are provided in the game, and the S3 plan Kernel was the game itself, which you experienced through Raiden, your avatar (who mentions doing a simulation of the Tanker incident to S- Pliskin
only if you do the Tanker-Plant selection in the game), Then there's the conversation at the end of MGS1 that says that Foxdie should kill off the last Shadow Moses survivors soon...
And the casting theater, MGS2 exclusive, which lets you swap character models in some cutscenes, likely implying that you could play the game as anyone selectable there and get the same experience.
Then MGS4 came around and ruined everything since the fans didn't really think like Kojima wanted them to (and those death threats sure did put pressure on him.)