The option to either render or prerender with effects applied at an individual clip level would be a helpful option.
Currently a render/prerender renders the entire selected timeline as one block but the facility to retain the individual clips after having effects applied, similar to "render in place" in Davinci Resolve, is currently not available.
The scenario for this is that a long video is cut into clips using scene detection and exported as individual clips. The clips are reimported then effects are applied. These paired clips are then processed in a third party app and finally reimported into After Effects.
Although obviously the footage could be exported and reimported if the scene detection is run on the processed clips it does not match the original scene edit detection and clips cannot be paired.