Perhaps there's other ways to solve this - for example if Construct could export metadata about spritesheets (i.e. the location and size of every image), then in theory some external tool could take a folder of individual image files and paste them over spritesheets, and that could be robust against future changes to the project. It would keep the benefits of spritesheets and only need a minor change to Construct, exporting some extra info it already has.
I know for sure i won't be making a tool like this. Way beyond my skill level, but if someone else or Scirra makes it, im not opposed to instructing the users to use it for modding.
Of course telling them "replace the pngs if you want to change the art" is much more straight forward but i won't keep beating the dead horse.
Oh and one comment about some users wanting modding and others not wanting it. Steam allows the developer to distribute different versions based on the user's preferences. So perhaps the more performant (spritesheet enabled version) could be distributed like that :) (not applicable for web platforms, ofc. lots of considerations )