Something that has never occurred to me, I just realized.
Kanto's Cycling Road is raised. It is a slope, obviously; that's why you go down it faster than you go up.
But I figured out the reason for that: under it is water. So it can be assumed that it is high enough for large boats to go under it.
The basis for this?
If it wasn't, the S.S. Anne would be completely locked into a small little pond. It has to be able to travel under it or no one would have built that boat there.
(And then I guess it has to be assumed all the rocks that form the borders of Routes 19, 20, and 21 are... not an issue for the ship to travel over. I guess.)
@The_T it's sort of a funny quirk of keeping the kanto map largely the same over time. stuff that you wouldn't really question in a game boy game suddenly becomes a little questionable when examined as a connected region. this is the most reasonable explanation i've heard of how the cycling road is positioned