Any idea what the darker colored sealant might be that I need to deal with? Would you remove it or tape over it?
Folks put all kind of stuff on roofs to seal them, I had asphalt on mine. What you have appears to be caulk (and probably contains silicone). I'd use some 3M caulk remover and mineral spirits as a final wash. There's no short cuts with this roof sealing. If you leave the old stuff on there, there's a pretty good chance anything you put on top will peel off with the failing stuff.
Also, any kind of roof topping you apply, short of a LineX style material, will not seal your roof.