OK so here is the most automated way I can find to batch export from AE. This works in CC, may work in older versions but cannot test.
Setup:
Open any dng and change any settings that you want to be used on all footage. For me this would be setting white balance to auto and camera profile to VisionLog. Now on the bar right above were the adjustment controls are, labeled "basic" on the white balance tab, click on the part that looks like page with a down arrow. Once in there choose the set new defaults. Now the current settings will be used from now on. Note the defaults will only be used on footage never opened with ACR on the computer. ACR must store the settings used somewhere and will remember what was previously chosen.
Create a output preset in media encoder and/or a output module preset in after effects to use during export.
1. From file menu choose scripts->smart import.jcx and navigate to the root folder that has all the footage. This script will import any file it can in the folder and is recursive so it will import from nested folders as well. It will open ACR for every sequence so you will have to hit ok for every sequence. You can also put something on your keyboard to hold down the enter key if you don't want to sit around a hit ok for every sequence.
2. Select the first dng sequence and hit ctrl+alt+g to go to the interpret footage dialog. Make any needed adjustments.
3. With same sequence selected hit ctrl+alt+c or goto interpret footage->remember interpretation.
4. Select the rest of the sequences and hit ctrl+alt+v or go to interpret footage->apply interpretation. This will apply the adjustments done in 2 to all footage.
5. select all sequences and drag them onto the icon below the project window that looks like a film strip and choose multiple compositions. This will make a comp for every sequence.
6. click on the 8 bpc button and choose 16 bit or 32 bit and save.
From here there are 2 options export from AE or Media Encoder. After effects is faster especially if you have multi-processing turned on, media encoder does a better job of encoding. If you are writing out intermediates in something like DNxHD I would use AE, for finals in H.264 I would use Media Encoder, etc...
7. AE: select all compositons and hit ctrl+m or composition->make movie. With all outputs selected in the queue change the output module to the preset of choice. They will all change at once since they are all selected. Go to scripts->change render locations.jcx and choose your output path and hit render.
7. ME: select all comps in AE and drag them into Media Encoder, choose preset and press play.
That is it, using this process you can deal with a large amount of footage fairly easily.
