I have fit the RJC down pipe on a few GN's and never had a problem.
There are other variables like type of header, turbo housing, suspension that can cause alignment issues.
Simple fixes can be to open the 4 holes in the DP for adjustment as well as doing the same to the turbo flange holes on the header. This will allow the turbo to swivel a little and move the end of the DP away from the frame.
I have seen this interference issue many times also caused by aftermarket turbo housings having the bolt pattern slightly off from the original Garrett housing.