The photo isn't clear, but to me it looks like the spoke you are holding should be able to have a nipple threaded onto it. Even if it's 1-2mm away from the surface of the rim, a nipple should be long enough to bridge the gap and thread a couple of turns onto the spoke. To get the spoke closer to the rim, you have to pull the opposite spokes and the hub towards the nipple hole that you're trying to thread into. The slack in the other spokes and the unseated nipples will cause them to get stuck in an odd place. You need to wiggle them free and pull on the hub to get the spoke you're working on closer to the rim.