I may be a moron, but it sure looks like the OP's image posted at TBN is the same as what whitetiger posted, and that the motor is on the top.The "diagram" the OP refers to is a drawing posted on TBN (copy posted here below). The HST unit shown is oriented the other way up from the diagrams in the Kubota parts lists - hence all the confusion about upper and lower.
Once we get past that, the "stop bolt" in question locates the motor's thrust plate to keep it from rotating. The plate's angle is fixed - the motor slippers slide on it as the motor block rotates. To keep the thrust plate from rotating, a "stop bolt" engages a notch on the edge.
The stop bolt is important because the sippers need to ride a film of oil constantly to dissipate heat and prevent wear. If the thrust plate is allowed to rotate, the sliding surfaces would become damaged very soon.
Theoretically its possible the "notch" could come back into view, but it's a long shot and risks scratching something.
View attachment 62480
BTW, the actual "swashplate" is part of the PUMP assembly and is not really involved in this.
The pump's swashplate moves - tilting forward and back with the pedal linkage. The MOTOR's corresponding thrust plate is fixed - the angle doesn't change. Its sometimes called a swashplate because the slippers move in and out as their block turns. Kubota just calls it a thrust plate.
Why do you think the image that the OP posted at TBN shows differently? This inquiring mind wants to know...