I haven't had a problem with focus, but try it and see how it works for you. Here is one of my references that led me to doing this (can't find the other):http://www.kennethleegallery.com/html/scanning/index.php
Worth reading the whole article but the relevant part for this discussion is:Film Holders: Flatness, Focus and Newton's Rings
Epson film holders do a good job of keeping the film flat. Because the film sits above the glass, they also prevent Newton's Rings: concentric lines caused by interference. However, Epson film holders crop the image and being shiny, they cast reflections onto the edges of the image. To avoid these problems we can use a holder from BetterScanning.
With either Epson or BetterScanning holders, the scanner automatically sets focus to a few millimeters above the glass, but BetterScanning holders are adjustable so you can find best focus. For a personal sample of how the BetterScanning holder improves focus over Epson's holders, see my before and after images here. For Better Scanning's comparison samples, click here.
Another option is to tape the film directly on the glass, emulsion-side down and use the Epson "Film Area Guide". Depending on the film, Newton's rings may not appear. When we use the Film Area Guide the scanner focuses at the level of the glass.
Therefore if Newton's Rings are not a problem, we can get very good scans by taping the film directly to the scanner glass. I use blue painter's tape for this purpose: because the film is placed emulsion-side-down, the tape never damages the film emulsion.