The section you quoted talks about “inlet” boundary conditions. Check the description of mass flow rate for the “outlet”. For the outlet BC setup, there is no option to set the flow direction.
I believe that by prescribing an outlet mass flow rate BC, you’re enforcing the flow to be normal to the boundary. Alternatively, changing the inlet BC to mass flow rate and outlet to a zero static pressure would be a better option. If you know for sure that the flow through the existing outlet would not be normal to the boundary, you should either (I) move the outlet further downstream and prescribe a zero static pressure condition or (ii) change the outlet to opening.