. On reexamining your sentence, I agree with your original assessment. If it is constructed correctly, then 'it' must be a pronoun referring to something previously mentioned. Otherwise, I suspect that the writer chose the wrong voice:
It may be proven in the future that neither falls short of evidence or that some synthesis of the two theories is plausible.
Hi, Although you give no context, it doesn't seem natural to say that a theory falls (or does not fall) short of evidence. Perhaps you should say it another way.