Yes to all of this. His view of Gene gradually shifts from seeing him as a mere tool to seeing him as a person with a mind and soul, and you can see the moment it literally clicks for Scrooge on the screen. To me it’s an emotional scene because the full weight of how messed up the situation really is hits him full force that he speaks with difficulty. And Alan Young gives Scrooge such a wonderful emotional range.
Scrooge is horrified, guilty, and saddened all at once by the realization of how horrible Gene’s existence as a genie is – a sentient person (a kid) forced into doing horrible things, and suddenly all the fear, paranoia and attachment to the boys and Webby started to make sense.
Let me tell you, Scrooge must’ve been freaking proud of his kids later on because he didn’t forget how hard they tried to protect their new friend and make him feel loved for who he is as a person rather than, well, a miracle worker.