I think you are supposed to have sound deadening material there. The studs have a plastic nut to hold it on If not must be something from the inside..
Ah, had to go look at my truck and stare at the picrue a bit. Those are the mounting studs for the PCM, guess they just stayed as a part of the body until it changed later. Pretty sure the 03-05 trucks all shared a common body build.
Vacuum resevoir not servo,we have used remote resevoirs for vacuum storage for many years
PCM is on pass side firewall. What the studs are for is the cruise control servo unit as seen in my pic. 04.5 and up the cruise control is controlled by the ECM