The Experiment, Bob Relationship
It looks to me that Bob was not born of The Experiment (unlike all the eggs that are clearly visible in the spewing scene), but instead a parasite much like with Leland and Mr C., or, a companion of The Experiment. It could then be possible, that The Experiment is what is trying to search for Bob to get him back (and the one who spoke with Mr C., pretending to be Phillip Jeffries).
Also, do we believe The Experiment was created during that atomic explosion. The scene does not state that an atom bomb went off (for the purposes of the fictional history of Twin Peaks). What if The Experiment, Bob, or perhaps some mating ritual caused the explosion?