I had a different problem than this but i just found a solution that could fix multiple things at same time. my original problem was that i have some cities on a larger isle and some on a continent and a trieme on the caost sea tile that lies between the land masses to bring caravans and whatsoever to the other shore. problem is that it's hell annoying to move your units manually to the ferry and unload them manually next turn and send your ships to sleep again and a raod like connection is available much later with joyoos SeaTunnel mod.
Solutiuon: rename SeaTunnel to Ferry, make them available with first transport ships (not with working boats maybe since they don't look like they could carry much; the trieme would build the ferry) and our both problem is solved. i've looked in the SeaTunnel files and it seems there are only few things that would need to be altered: apart from the movement cost it's only graphics. i though to make the 'sea raods' a dashed half transparent blue line (like ship routs are usually marked on maps) with a small trieme in the middle... but ahm.. how do i modify the .nif files??
this shouldn't break any balance since this transport option is anyway available for units - it's just more nasty. enemy units cannot use these ferries if they don't have a special promotion, so it's quite realisitc. and since triemes are not allowed to pass oceans ferries cannot be builded on these tiles unitl later ages. well and if people play with the option that allowes that, one could increase the build time of a ferry to 4 turns so the trieme has a very good chance to sink before finishing its work.
and maybe for the future: since there are faster transport ships later on the should be different ferries like there are different road types. graphically they'd only differ in the miniature ship displayed in the middle perhaps.