Turbulence definitely creates more issue with denser fluids. Fluid Dynamics was not one of my favorite subjects, but I did receive quite a bit of instruction while in school for engineering.

With air, I wouldn't expect any issues from a few mm reduction in diameter, even without treating the edge. With the end facing the flow being blended and smoothed, and the end facing the motor left sharp, or even undercut, the change in flow should be minimized. There is friction between the incoming air and the side of the duct, which means that the air at the edge is already moving slower than the majority of the air moving through the pipe. From that, I would reiterate that the EGR pintle in the stock setup causes much more disturbance and turbulence in the air flow.

As for the mating surfaces, I'm sure some RTV gasket maker would go a long way towards sealing that face. I also have some specialty anaerobic gasket maker from Loctite/Henkel that may be well suited to the job. It cures a bit harder than RTV but still has a little give. It also sets up very quickly once you close the gap between the parts.

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