The film area guide's main purpose is to allow the scanner to calibrate correctly during the initialization routine. It doesn't change the focus. Focus is changed by the selection you make in the software which doesn't do any actual focusing but just tells the scanner which of the two fixed-focus lenses in the optical system to use. One is supposed to focus at the scanner glass level and one is supposed to focus at the default holder height level. Depending on your particular scanner, it may or may not focus at that height.
Doug
Thanks Doug, you are correct, which I saw when I finally got off my ass and actually looked at things.
I did a couple quick and dirty scans of a 4x5 negative at 2400 dpi with my V700, once with the film holder and once with the film area guide with the negative emulsion side down on the platen and a piece of Tru-Vue AR glass on the top. Results are very close with one side being a little softer with the negative holder. We are talking about pixel peeping a 10,800 x 8600 px image at 1:1. I have not tried tweaking the negative holder height, it's just out of the box setting. Anyone who's interested, here's a zip of jpegs of the files after rough exposure/color/crop matching and flipping the platen version in Lightroom, about 100MB.
http://www.ahfairley.com/misc/Scanner.zipAnyway, it would seem that except for any improvement from use of fluid between the surfaces, there's no real advantage from the FMA over Mark's "glass on film" because I read that the FMA does not have any height mounting adjustment (well, I guess there would be an advantage if your factory focus setting for the film holder/FMA were spot on but the Platen setting was off; and if the FMA needed to be farther from the platen to get best focus you could always fix that with shimming). Does the use of fluid per se give improvements, or is it just a flatness thing?