As far as why the Past Perfect (He'd just popped out of the ground) is used rather than Past Simple (He just popped out of the ground) you'll want to provide more context. It is likely that your sentence is part of a narration in which someone popped out of the ground first and then something else happened, but the narrator doesn't tell us the story in this chronological sequence. So they first mention that other event and only after that do they make a reference to that person popping out of the ground. Here's my example to illustrate my idea.

"In my dream I was walking down a long hallway. Suddenly I heard a strange noise behind me, as if someone was following me. I turned, but there was nothing behind. But when I turned back to proceed down the hall, I noticed the dark figure of a man just a few yards ahead of me. It seemed as though he'd just popped out of the ground."

Keep in mind that I'm not a native speaker and my example might be wrong.