Google books actually shows a constant decreasing usage of the expression in the first instance in the first instance from which probably the fact that some users find it “unusual”.
Moreover, M-W suggests it is a formal expression:
in the first instance - idiom (formal):
before other events happen : as the first thing in a series of actions You will be seen in the first instance by your own doctor who may then send you to a specialist.
- You will be seen in the first instance by your own doctor who may then send you to a specialist.*
For what it is worth, I am quite familiar with this expression and I don’t find it unusual.