I think you're right in both posts, Bronson. You're right that most beginners don't know how to 'slow down' their movements and yet also stay true to what would happen if it was all happening at speed. I think that learning how to do this is a big part of learning Aikido. By learning to go comfortably back and forth between fast and slow, you can carry lessons from one over to the other. We can't expect beginners to know this, but we still basically want to train for the physical realities of the fast speed and not the slow.
I also think you're right about the second thing. Think about it this way: even if it wasn't a question of learning vs. instinct, still different people will have very different reaction times and very different coordination skills. You can't assume uke is going to see your atemi and you can't assume he or she is going to know what to do about it and you probably shouldn't even assume that you are strong enough to hurt them with it. One of the teachers at my dojo told a story of trying to restrain a drug user in an emergency room. Someone got a good solid nikyo on the guy and then the guy just used the nikyo to throw said somebody across the room. The guy's wrist was totally shattered by this, but he was so high he didn't notice and just kept fighting.
Nothing is more effective than being able to ready your opponent and to see what will and won't work on them.