Ahh, you're right. The reason A[0] on the CPU isn't connected to the flash chip is because it's addressing -words-, which I didn't exactly realize at first. I got myself good and confused.
Apparently when you access the flash chip in byte mode, you set "A[-1]" (high or low byte in the word) via D[15] when you're writing or reading. Odd nomenclature in the AMD doc.