I'm not sure Fake Kraid is supposed to tie into anything storywise, seems more like a joke being played on the player to fool him/her into thinking it's the real Kraid considering he was that small in Metroid 1, only to surprise the player by the real Kraid being a skyscraper.
Also, Kraid is shown as somewhat mobile on his feet in Super Metroid, I guess if anything is in his way he could simply break it down to make room for himself.
When I was playing SM for the first time, I actually thought that was the Real Kraid, something like: "What? I thought he was huge!"
Btw, as some people said before, the Palutena-Ridley support is really the same thing
BOTH have the stage where they are fought
BOTH had copies of them shown in the Direct
Palutena was said to "watch over the arena", yet this implies playability status and "Samus' trauma may appear at any second"(not how it doesn't reference the stage) means boss status
They are the second most important chars from their franchises, and let's be realistic, no one from their games will get before them
Never mentioned by name("goddess of light" and "Samus' trauma")
And finally, Sakurai recognized that they are sister series during development, even by making a reference on how the Komaytos look like baby Metroids
Also, Palutena is bigger than Ridley but no one really seems to care about FACTS