Stephen Allen applied for the Heathrow Planning Permission on 25th March 2013.
London Borough of Hillingdon - Planning
The Davies Commission looking into the possibilities for runway expansion in the South-East only had its terms of reference announced in November 2012 and Heathrow issued its initial proposals to the Commission in July 2013.
I think it is reasonable that the planning permission scheme might have been developed without assuming the likelihood of a full runway expansion.
And it is understandable that Heathrow may decide not to incur the expense of implementing the original proposal if will only be of benefit for a year or so before it is thought that it will be subsumed in the work to create R3.