If the basic setup gives an advantage to P1 (and I don't know that it does), a simple modification is ready at hand. Just move one of P1's scepters to their middle cube. Do the same for P2, making sure that everything is kept symmetrical.
In addition to this, I would also recommend the simple setup variant which I have described in this thread: The View From Down Under. It allows scepters to pass beneath the matrix and up the other side without a first-move victory for P1.
Or moving an axiom to capture the center square, which, at least for me, has always ended up with the starting player being ahead in the square count.
I don't understand this comment. There is no "center square". There are 2 upper middle cubes, one dark and one light. If P1 moves their scepter to the dark or light cube and P2 follows suit, where's the advantage to anyone?