Running the pipe to the bumper opening is the most convenient configuration. The space vacated by removing the resonator leads towards the bumper opening. It's actually very convenient and easy to do it this way.
One worry now is the possibility of water being driven up the pipe to the filter. I think I am going to add a mesh screen at both ends to minimise this... I also need to make more drain holes to allow excess water to weep out.
I should have thought of doing this before putting the bumper back on - I hate having to take it off again.