As far as I know, the Epson V-700 does not moves the focus. It has two lenses, one focused at the glass plane, used with the film area guide or opaque originals (called the high resolution lens) and the other lens focused 3 mm. above the glass plane, when you use the film holders (called the super-high resolution lens).
Silverfast has the option to switch between film area guide and film holder for the Epson V700. If you go to the general tab in the silverfast control window, you have the following options for "Original": reflective, transparent and transparent (full area).
Transparent (full area) = high resolution lens
Transparent = super high resolution lens
You should get the same focused results with Silverfast as in Epson Scan, provided you use the correct settings.