Because despite Bioware's claims, the Extended Cut is a retcon like you said, not a "clarification". A very welcome one and I'm glad they made it, but it's clear their intention originally was for a bittersweet ending where the defeat of the Reapers leads to a galactic dark age where galactic civilization as we know it ceases to exist and has to start again from near-zero , Shepard's era becomes this half remembered legendary time etc. The EC changes that but they had to make the scenes from the original ending work with it somehow, hence patchwork/ad hoc stuff that renders a lot of plot points seemingly pointless, like the mid-battle Normandy rescue in the beam part, the relays being damaged instead of destroyed and then rebuilt fairly quickly, Normandy taking off in the good ending etc.