You are correct in that the little 5mm bolt only holds the rotor to the hub, nothing more. It is the actually tightening of the wheel against the rotor and thus against the hub that makes it fully seat.
That is why torquing the lug bolts in a star pattern is so important. This process pulls the parts together evenly.
It is not that uncommon to have a wave or a high sport after replacing rotors and pads. I just think many don't bring it up. One simply small blot of grease is all it takes. Try BrakeKleen or other brake part spray cleaner, but my guess is that if you are already feeling it in the pedal, you will need to turn the rotors. It is rare in my experience of rotors that are waved to cure themselves.
If you are game, you can try multiple very light brake applications to take off the high spots, but I think you are headed for a rotor turn.
You can also try sanding the obvious spot on the rotor. You want to use an emery cloth or other similar type abrasive. Be sure to check the inner side.
As a tip, whenever I replace rotors, I always make sure the mounting surfaces are clean and smooth. I then apply a light covering of these mounting surfaces with anti-seize.
Keep us posted,
'03 E320 Wagon-Sold
'95 E320 Wagon-Went to Ex
'93 190E 2.6-Wrecked
'91 300E-Went to Ex
'65 911 Coupe (#302580)