The Romans, as I am sure all other literate (upper class) people were capable of expanding the application of a word and giving it multiple meanings. Using Helen's example of our word fenestration, from the Latin fenestra, an opening or hole. Romans also used the word to indicate an opportunity, and an occasion, as well as a window.
Penetrale, an inner place, became associated with secrecy, and shrines.

Penis, penitent? No, from different Latin words. At one time a plural for penny in English was Penis. Lots of room here for inventing false associations.