I'd warn against modding out every little inconvenience like that or it will soon become overwhelming and difficult to keep track of. Clothing actually affects combat quite a bit, and players may not enjoy having their adventurer completely naked and unprotected. Who knows how many specific bugs like that Toady has already fixed for this next version or will be fixed in the following releases. That bug in particular won't require Toady change any raws, and will likely immediately take effect when the world is loaded in the version which fixes it just like ghosts do when old saves are loaded in versions after their implementation. However, if we remove clothing from the entities or remove the raws for them entirely, it will be impossible to change without a regen.
Sorry, but that honestly sounds like a terrible idea.
Also, those older prototypes with civs on the coast were generated with my mods installed rather than vanilla (was only testing landscapes.) The cities you saw belonged to a seafaring civilization of birdmen, not humans.
I'll try to repaint the edges of the ocean, but I did that specifically hoping that sea serpents would actually spawn close enough to the shore to be enjoyed by players (because savagery can change within a biome, and still affects creature spawning), which demanded the shoreline itself be savage. It was lazy, I guess, to not zoom in and detail the shore itself as neutral.
Also, it's unbelievably difficult to get it to generate an ocean as a good biome, since the entire ocean will be either good, evil or neutral (it all counts as one region, ignoring temperature and savagery changes that can affect some creature spawns). Evil seems to override good, but fortunately, all you really have to do is generate it over and over again until you find a seed that works, which I will definitely do since skeletal whales aren't a joke (skeletal groundhogs are pretty terrifying as well, in some cases.) Maybe it'll make for an even better river and mountain valleys...