My supposition earlier was that even if new rails or roof assembly fixed the problem, it would be temporary because the same friction issues would return. Unless some gasket or separator rubber washers or some such was installed, it won't correct the problem, which is a design defect, that allows the metal frame of the sunroof to rub against the metal frame of the car body. Unfortunately, the metal frame of the car body flexes and vibrates when the car is in motion. There is so much contact area that no matter how solid the Stinger may be (probably above average), the creaking will occur.
So, as I asked others above, please get the dealer to tell you exactly what process was followed and what material(s) were used to separate the sunroof rails from the car frame during the replacement process. If they don't know, or the answer is none, because none was there from the factory, then I am not surprised the problem still exists. It is just a matter of time before it appears and in a manual installation of a sunroof the mere slight over-tightening of some bolts (compared to the robots in the factory precise tolerances) could make the problem appear immediately or make it worse than it was previously.
There is supposedly some gasket or separator material being tested/used in some country(ies). We need this everywhere before KIA pulls another fader problem fiasco (erroneously replacing entire audio head units at tremendous expense and hassle to owners [entire dash and console has to be ripped apart] when it was obviously a software issue all along and later updates to the EVO software did fix it). Inserting properly designed rubber washers under every connection point (six, I believe) to prevent ANY contact between the metal parts solves this problem. Cost: $2 for the parts and can almost be done DIY. Of course, it would be best for dealers to do it.