I'm not sure about the physiology involved, but measuring sleep stages does involve inferring them from body movements, among other things. Accordingly, it's quite likely that having an Apple Watch ON YOUR WRIST while sleeping makes the estimates much more accurate. Frankly, I have NO idea how an iPhone sitting in its charger can tell whether or not you're even asleep, let alone in what stage.
However, I CAN tell you what works for me. At least a half hour before I retire for the night, I'll put my watch on my charger, then put it back on my wrist just before going to sleep. For this to work, I must ALSO manually "start" the watchOS "Sleep" app ON THE WATCH. If I don't, the iPhone might guess WHEN I was sleeping, but not make ANY attempt to assess in what stage of sleep, and those estimates are often dramatically incorrect. So, in the end I think Apple is just trying to give users the most accurate data available FROM the pairing. I DON'T know, however, why it's necessary for me to take that extra step of "opening" the app on the watch just before I go to sleep.