What you're asking for will have a major impact on the architecture and it's not someting I think that will be feasable.
Where is what I can do, there are post conversion custom commands available right now in MCEBuddy that can be configured through profiles.conf. I can introduce a pre-conversion custom command which will run before the remuxing happens. You can
run your donator comskip there and if it generates a EDL file then move the original file to a monitored folder ALONG with the EDL file and MCEbuddy can pick up from that moitored folder (it will skip running comskip again if the EDL file is available).
You can write a batch script for this and then run the batch script from the pre-conversion custom command section. Will that work for you?