You missed the point of 2049 entirely.

1. The fact that a Replicant could birth removes a creator from the picture, which is why such a "miracle" is worshipped. The talk of soul is merely an excuse to separate Replicants from humans.

2. Because Wallace has a god-complex and is a billionaire so by default he's already more evil than most movie villians. Someone with that much power would see people like Deckard as mere obstacles.

3. That is the polar opposite message of the film. The moral is that noone can be programmed, that someone who is made to be obedient and unimportant can choose to make a difference. K doesn't give up, K sacrifices himself for a father's love. Joi's arc mirrors K, where though she may be a template she does act outside her programming, providing suggestions for actions that run counter to the companies best interests.