Tomatoe, tomato. The E at the end of the word generally reflects hardening/lengthening the preceding morpheme (rid, ride; cloth, clothe).

This is a good example of how language evolves because tomahto has not ever been a correct spelling of tomato, and tomatoe is an incorrect spelling derived from making tomato plural into tomatoes and then (incorrectly) dropping just the s to make tomatoes singular again. A mistake based off of a mistake. So while intelligible if incorrect, who's to say if it's wrong?