If you have quality aftermarket cats installed and the O2s in the proper positions you should be able to pass with the O2s relocated but not 100% sure. I think the EU2 factory flash should take care of any software issues if you still get codes.
For what its worth, my previous e46 with headers (I did not own it at this time) did not pass visual in NC with magnaflow race cats and rear O2s relocated with no codes. The tech said it was not legal to relocate cats from their factory position and added this to the DMV system so the car had to be swapped back to stock exhaust to pass. So it may depend on who looks at it even if there are no lights.
I would also suggest it is worth the extra money to get metallic core cats, the ceramic ones are cheaper but very sensitive to any impact (a concern if lowered) and my prior car blew the honeycomb material out of both ceramic core magnaflow cats after about a year.
E46 330i ZHP 6MT
E46 330ci 6MT
E92 335i 6MT
E36 M3 5MT
E46 323ci 5MT