Hammering the body down onto the dowel guide pins:
I'm not using the dowel to aid the joint, I'm simply using them as a guide so I can cut the timber close to the desired size, minumising wastage, but it also stops the timber from sliding all over the place when I clamp it, which I can assure you, the couple minutse you spend making, hole punching and drilling the guide holes definitely makes up for the hassle of glamping unguided timber and removes and chance of a position error. I also make sure the pins are located in a spot where I will either be romoving wood, or where wood won't be carved, so they'll never be seen.
Body in clamps:
I clamp alternating side to side so the clamping pressure is spread even. If you only clamp from one side, the pressure pulls to that side making a imperfect joint.