I mean, how could the TNG Tech Manual author seriously claim to know the function of an item better than the person who had actually created and put it there?
In dealing with fiction, this sounds perfectly plausible and practical.
OTOH, the same lot of people that wanted to give the saucer a deflector by appropriating a series of windows similar to those on the TOS saucer bow were later responsible for turning those TOS features into pretty explicit windows...
As regards the color, remember that we never saw the saucer at warp from a forward angle. The squares might be lit blue only when in use, with the golden glow matching the standby color we witnessed in the TOS movies.