If you are willing to go back aways, many words have alternative spellings with the same pronunciation. Take the fishy spelling of The Compleat Angler, for example. But some modern words have two current dramatically different spellings pronounced alike. One example is the spellings of controller and comptroller. In The Way We Live Now, Anthony Trollope has one character say vittles and another say victuals. Note that these are not homonyms because only one word is being spelled.
In saying "two quite different spellings," I am trying to eliminate spelling variants such as today vs. to-day, colour vs. color, or the example I gave, complete vs. compleat. In such pairs, everyone would naturally pronounce the two spellings alike. That's not the case with vittles vs. victuals, hiccup vs. hiccough, or controller vs. comptroller. Indeed, some people (not I) do not pronounce the last pair alike. So I do not believe that my question is in the same spirit as a previous question. Though there is a distinction to be made, it may be that English has no word for this distinction, and all that can be said is that the words I'm considering have extreme spelling variants.