Er... what? The game is straight up lying to you, according to this ending, by having the entire thing not be the truth. We don't know what really happened. I imagine Bioware's going to come along with some DLC that shores up the whole, "It was never real!" thing, but it still makes it bad writing. Do you remember how mad people were at the end of... that one TV drama that was all just a dream? (The name escapes me at the moment. It was a medical drama.) Yeah. Nobody likes that.
I can't tell you why Shepard was "alive" in the rubble on Earth. I can't tell you why killing the Reapers doesn't kill Shepard. Do you know why? Because it's poorly written and never explained. Nobody can explain these things except the writers. The fans certainly are attempting, and I imagine they're giving the writers a TON of ideas for that $14.99 True Ending DLC. Thanks for that, fans.