I've done an edit in a Premiere CC2015 1080p sequence which is the resolution of the footage. I now have to scale up and recompose some shots (some shots to 135%). I hoped that if I nest the whole 1080p sequence into a 720p sequence then Premiere will be smart enough to calculate the actual relative scale when rendering out (so the scale would be more like 115-120%).
In my test of the more modern CC2015 it would appear that Premiere's render order/system does actually do a pretty good job, the nested sequence is only slightly softer (barely noticeable unless you look really close at a still frame)
First test shot blown up to 135% in a 1080p sequence, that sequence of which was then nested in a 720p sequence and scaled down (as a nested sequence) to 67% to fit. Comparison shot was the original 1080p footage in the 720p comp, scaled down to 80.5% in order to match shot size composition exactly.
So I'd conclude that it's fine to scale and nest as required with close to unnoticeable results, which is far better than rescaling every shot in the 1080p edit down to make a 720 edit.