What matters is the center points, because like for land regions, travel between sea zones is largely assumed to be from center to center (with exceptions for embarking and landing, so a next-region ship trip does not actually go via the center).
Do you mean, for example, that for a trip from Port Raviel to Paisly the assumed boat path is outlined in red, but only the part in yellow is actually used for calculating the time, and the parts in red are fixed embarking/landing value?
That still makes it quite a convoluted path.
