What difference will there be in my "baked beans" if I cook them on the stove top instead of baking them?

I mix onions, green peppers, bacon, liquid smoke and brown sugar in my VanCamps pork and beans. They turn out the best when everything rends down so you can’t really tell what the individual ingredients are.

Can’t I get the same result by cooking them on the stove? I think I could also control it better.