Flooded Mine is a ride they know they shouldn't mess with too much. Turning it into just another dark ride would be a mistake. The new dark ride at SFStL looks nice, but I guarantee it won't feel as magical and timeless as a trip through FM. I'd love to see them add a new dark ride to the park, but Flooded Mine is more than just a classic. It's a good ride that everyone still enjoys and it really embodies the SDC character.
I feel like they could have theoretically done either/or concerning the hi-lo silos/fire tower question, but the current setup just works really well. With the right theming and story, you can make a lot of things work, but firetower is a good visual centerpiece for FL. I agree with chittlins that having them where they are helps families to stay together as much as possible, which is a big deal.