DPX if it needs to be perfect and re-renderable. PNG if there's mostly solid flat colour, JPG if it's more photo or video based. Again it doesn't always cause issues, but sometimes the Premiere cache will get stuck on the old frames and it might flicker back and forth on export. I'll have the image sequence in Premiere along with any accompanying audio, but I'll close Premiere before I render new fixes in AE.

I don't know if overwriting is ideal, but if its something like a typo I know I'll never need those frames again so I don't see it as an issue. I might notice small little fixes or get some feedback about some text changing in one part, so I'll just need to re-render those small parts and overwrite the existing images. Like right now I'm working on an awards presentation and its a pretty heavy render. This is the best option if you're doing anything that's kind of long (like 1 minute +) if its made up of multiple chunks. But I do think it would be a good idea for you to do a test run and see if renders are faster and/or better quality compared to a direct render. If you have a system that is working for you and you are happy with the results then by all means carry on. For many they are not going to have freeze up issues, but there are far to many posts here about this very issue, 'My render is low quality', 'Its taking hours for a couple minute video', 'Help render has crashed' and so on. Personally I see a noticeable difference in quality when I do it as a two step process and render speed is most definitely increased taking less time rendering twice than rendering a single time directly to mp4. Project size is irrelevant for this issue, however, as we all know(or at least we should all know) larger projects are going to take longer than smaller ones just from the fact that they are bigger so for this case we are just comparatively speaking for the same sized project. No need to render a new high res file or having to render from the AE project.

One other plus is once you have a high res file you can now create multiple formats using the single high res video file. So you may wish to visit the thread again. Some of the other comments here have touched on this issue in a little greater detail.

Aftercodecs freezes