I think the challenge here lies in what you actually want to do, which is affect the intrinsic Scale property back in After Effects, so even with a successful workaround, it might still fail you in After Effects. For example, you can get the Adjustment Layer trick to work by making your Premiere timeline larger than 1920x1080 and creating an Adjustment Layer at the updated Sequence size. For example, if you changed your Sequence Settings to 3840x2160, dropped a UHD Adjustment Layer in, then added the Transform effect scaled down to 33.3 percent, you would be able to retain the original quality of each of your clips. (Doing this avoids this issue you saw earlier which only scaled down the cropped portion of your sequence.) Then, you could nest that now overly large UHD sequence in a 1920x1080 one and everything would appear correct again.
So, workaround successfull! Except try sending that to After Effects and see what happens. I can't imagine it would work properly.
What about this instead?
- Import a sequence into After Effects.
- Create a Null Object in the center of the comp.
- Parent all of your scaled up clips (which should import into AE at 294%) to the Null.
- Change the Null's Scale parameter to "100/2.94" which will give you a more exact number than 34%.
- Delete that null.
- Are all the clips' intrinsic Scale properties set to 100%?
This is clearly a huge headache for you, and a lot of testing needs to be done to figure out a practical solution (if one exists), so I can't say for certain that what I just said would work, but I'd like to think it could.