The inlet and outlet may be the same face of the rectangular pipe or may be on different directions. Assume that entry length has been taken care. If someone has a simulation of the velocity profiles, then please share.
if inlet and outlet is not located in parallel (with flow direction), it makes pressure difference between inlet and outlet, resulting in different friction, velocity profiles or vortex etc., i guess.
Turbulence pattern, vortex position and evolution, friction....
I assume you are interested only in incompressible flow model. There are many papers published about the channel with rectangular section, but you should be more clear in you question. Are you interested in a laminar or turbulent flow? As a general comment, the outflow should be in any case located quite far from the inflow to let the flow developing. However, also prescribing the inflow condition is not so simple for a turbulent flow.
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