lets say you scratch your bottom to the fiber, gelcoat gone. Everybody says don't go in water without protecting it, by putting gelcoat back on it.
So we all know and understand the exterior gelcoat protects the inner layer of fiberglass from water.

What about the water in the hull, where all, or most fiberglass, is exposed to water? Besides the engine compartment being generally painted or gelcoated, ALL the rest forward is bare and exposed!
and many boats, maybe more cruisers staying in water, have a little or more water staying in the bottom of hull, and nobody seems to have an headache with that.

why not being scared of interior water as much as exterior water coming in direct contact with fiberglass?

Because when you scratch off the gelcote you expose the fibers of the glass witch can absorb water. The interior glass has a cote of resign over it to protect it.