I haven't used an Avid for a long time but I know it used to convert anything that you imported into the format that the project was set to. This can be slow, and if you get the settings wrong you have to re-import your media, you can't just change the interpretation, like you can in After Effects.
If the resolution is wrong then Avid will re-scale the media to fit. I'm sure After Effects will do a better job at this so you may as well render the correct format out of AE.
As for having more resolution in a square pixel image, this is true but if you are working in an anamorphic project then you are never going to deliver these extra pixels. You will have to lose them and convert to none square pixels at some point. If it doesn't happen in AE then it is going to happen in the Avid or at the export/master to tape stage. You may as well do it at the point that gives the best result, or makes the rest of the workflow easier.
I know that the way that Avid deal with media has changed in the past few years so I don't know if this is still the case.
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