The idea of using an intermediate language makes sense. In a way, the two versions of the program in language L1 and L2 are supposedly equivalent to a language that encompasses both L1 and L2.
Regarding the choice of the M language, I would not lean towards a machine language as such. On one hand, I agree that we need a language that expresses all the capabilities of both languages L1 and L2 in a way that is not ambiguous, on the other hand, it would be better if it is done in a short way to be easy to handle by LLMs. It is ok if the code does not exactly match at the processor level as long as it gives the same result in a similar amount of time.
The generic language I am thinking about would need to have all the basic features of all languages, so one way or another it would be able to handle char*, reference counted strings, garbage collection, explicit (de)allocation on the heap, lambda functions, etc.
Having one generic language would simplify the need for documentation. Basically the parts that would require some thinking would essentially how to translate features into a language that do not have them by default. Whether we use an intermediate language or let the LLM the task of noticing the differences in the languages, remains the choice on what to do when basic features of the language differ.
When converting from C to Pascal, would the translation use Pascal strings or continue with PChar? For internal values in methods, switching to Pascal strings could be simpler, but for memory structures that are exported, one need to keep the PChar for compatibility. It could rely on external libc, on a package, etc.
Conversely, when converting from Pascal to C, it may be needed to have reference counted strings in C to make the program work the same. It could rely on GLib to do that.
The IA could search the web for resources on specific subjects, get the most up-to-date method to do something etc.