Should I export DVCPRO HD 960 x 720 ?

Here’s the pipeline for my current HD animation project.

I work in animation programs like Flash and Toon Boom. I export image sequences at 1280 by 720.

I take said images into After Effects, where I composite the images and render them out as Quicktime mov files. The mov files get imported to my edit program for the final edit.

So my question is regarding the format of the Quicktime files I’m rendering from After Effects. One of the presets I have to choose from is DVCPRO HD 29.97. That sounds like what I want, but that makes my mov file 960 x 720 instead of 1280 x 720.

Is this a bad thing? Am I losing information, or is it just doing some rectangular pixel thing to my square pixel source images? These 960 files seem to play fine when I turn around and bring them into my 720p Premiere project.