60p proxies should automatically conform to the original's "Interpret Footage" settings when generated in Media Encoder
To sync 60p proxies with your original footage in Premiere when you’ve conformed the frame rate creates a big problem.
The proxy files don’t know that you’ve conformed the frame rate of the originals so enabling proxies displays the clip at a different point in time.
The only way currently to fix this issue is by initiating the proxy generation but then stopping it before the first file finishes and re-interpreting that batch of files. Then you have to re-connect that first file. You can't generate all of your proxies at the same time either. You have to pick out which of your files is 60p conformed to 24p (or whatever) and create those proxies as a a separate batch encode from 24p stuff. This drives me insane.
Chris Hunt commented
Davinci Resolve handles this process much more smoothly. Don't understand why premiere can't at least send the data to media encoder that the original files have been conformed to 23.976.