zinon and your experience with the test setup tell the truth -- with a Xantech system in place, it will not matter if you send a signal through the Xantech AND directly to the components. I have done this many times, as well as using multiple IR pickups in the same room, with total success. (Niles stuff will not work with multiple pickups in the same room. They can't give a reason that makes sense.)
As for the confusion when you are using a rear input, well, that is another matter. Sometimes a rear input disables the unit's IR sensor, but it seems odd that the front and rear signals would compete or confuse.
VinnyBag, what model Sony DSS had that problem? I don't remember seeing rear IR inputs on Sony DSSs.
As for the red neon story, my personal favorite was the guy whose IR system did not work for about an hour every day.
He lives in Malibu, which faces due south. When the sun is in the right position, the millions of reflections off of about a square mile of ocean wave crests make an IR signal that overpowers any IR that is more than about an inch from its component. He can't draw the shades, either -- they are IR-controlled Makitas!
A good answer is easier with a clear question giving the make and model of everything. "The biggest problem in communication is the illusion that it has taken place." -- G. “Bernie” Shaw