So my normal procedure is to bleed the brakes with the wheels removed to avoid any chance of contaminating the disks. The brake pads are spread using the plastic `keepers` that can with the brakes. Dimentionally those plastic `keepers` are 0.10mm thinner than the disk and using those to set up the brakes instead of the disks themselves may account for the difference in `feel` you`re talking about..

Is that any different than what you`re doing?