What you’re missing that is “red is an apple” is also possibly saying in a metaphorical sense that red is like an apple to someone - delicious, a treat, perhaps otherwise representative. In that way, the encoding of “is”’ is exactly correct - it’s an ordered pair of glyphs that imply a weak form of assignment or description. : apologies, replied to the wrong post, meant to push this up one.
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.