Why do gray axles appear black and black axles appear white and black in this manual? I've been looking through the parts of an old manual I have and I noticed the odd-length gray axles appear black and the even-length black axles appear white and black.

Is this just an artifact of the lossy compression and thick outline colors? It appears gray parts are outlined in black and black parts are outlined in white. I'm pretty sure this set came with standard axle colors.
I don't have this set, but used 8421 as a test. This set is also released in 2005.
Looking at the PDF you see the same color scheme of the axles, were the black appear to be gray and vice versa

When looking at the instruction manual

You see the normal colors, so indeed your set came with the normal colors and due to some bad scanning and compression the pdf got discolored