It's not possible to add a set of real InDesign footnotes, even by
scripting, as you are probably aware.
It is possible to write a complex script that would do this, though.
We do have such a scripting framework (it can work with two or more sets
of footnotes). However, because of the complexity, we do not offer it as
a generic download -- it has to be tailored to the requirements of each
book (for page size, location of footnotes, etc.)
If you're interested, I'd be happy to discuss further -- drop me a line
at admin id-extras.com.