The correct sentence would start with a capital letter: “Red is an apple.” This is also completely valid as in a cartoon character of an apple named Red. The subject being the start of the sentence compounds the uncertainty in meaning.
Yes, this is because there's no assignment happening up front w.r.t. the word 'red'. However, you'll notice the same kind of ambiguity for the word 'apple' in the reversed sentence, as the word 'The' can imply quite a few things following it.
