Note that you can do both 15/5 and 10/10 missile configuration with either route. 15/5 is guaranteed to be faster, though, as it speeds up Ridley battle immensely and allows skipping the long backtrack in Tourian, making up for the time spent to skip the lake missile.
For the record, HBJ'ing across the lake takes less than 30 seconds (unfortunately, I never had enough patience to make ~20-25 HBJs required to reach the end of the lake).