If x00 (00000000) is off for both, and xFF (11111111) is on for both, then we aren't using some values there, since we only have 4 brightness levels

Well, 4 brightness levels is 2bpp not 4bpp (which would be 16 levels). The static graphics files on the player (like the boot logos) store the values raw, inefficiently, using an entire nybble for storing only two bits worth of data.

The empeg VFD screen itself isn't even techincally 4bpp or 2bpp, it's actually 1bpp. But they do a 200hz time-dither to get multiple shades. Sure, they could do other values other than those four shades we already know about. But they are very flickery and they just aren't used for any of the static graphics on the player.