Yes, i think LSL will have its own dock, & direct route to MK, but there might also be an alternate at slower times where they run a bay lake route... in fact they may have that full time as well so people could just travel between BLT, WL, CFW & Back.
No we can't do that since the submarines require a track aka the way Rivers of America worked. Bay lake is too large and deep for that type of solution.