All studies should be directed at identification of potential differences between a biosimilar drug and a reference drug, and on assessment of their significance (being there such differences).
The phrase "being there such differences" seems like purposefully obfuscated meaning to me. And in the aforementioned case, being there such differences and being there no other such similarities, the parties to A shall... you get the idea.
There's nothing wrong with "if" in formal writing - I would write your sentence as:
All studies should be directed toward identification of potential differences between a biosimilar drug and a reference drug, and if there are differences, toward the assessment of their significance.
I don't like at "at" or "on" with directed in this context. As an answer on ELU explains, "directed at" has an aggressive tone. I hope that reprimand wasn't directed at me - I didn't do anything wrong! Directed "toward" is what I expect in formal writing. Note that "directed toward" is more common in AmE and I believe "directed towards" is more common in BrE and which you choose is a matter of style.