For all we know, he did meet Amy and Rory earlier than before in the rebooted timeline, with the Daleks invasions having never happened as a result of the crack in time.
Exactly. Amy's crack has got a lot to answer for.
The truth is, we can't take anything
that happened in Doctor Who prior to 2011 for granted, because Series 5 ended with the entire universe being reset. Not just implicitly, like with the Time War, but explicitly
reset. It ends, and begins again. So all events in the Doctor Who universe prior to the 2011 series are by their very nature now mutable and may not have happened exactly as we saw them.