the only thing I can tell you from looking into velocity stacks/bellmouths for use in internal combustion engines is that I believe the bell mouth works better if its raised off the surface. It scavenges air better IIRC
So it would work better if not mounted to the box on either side(neither flare touching the box wall), so the flare is extended into or out of the box at least 1" or a couple inches on both sides.
As far as internal or external shouldn't matter, as long as following the above. Just more available internal box volume with an external port