If you can’t do something via GUI, it won’t be possible to do via API either. Figma plugins can’t add new features to Figma, they can only utilize and automate what’s already possible without plugins.
To help you better understand why this isn’t possible: in this specific case, adding something like scaleFactor to instances would require additional code on the Figma side to process and display the effect of this property that doesn’t currently exist. And plugins can’t add this code by themselves (that would require plugins to be integrated more closely with a rendering & file processing engine).
You are welcome to vote for the following suggestions which would help achieve what you want: