I think that what happens is that you get an offer based on the item's basic value (i.e. ignoring or undervaluing any magical component) modified by your merchant skill. It's a long time since I tried this, because virtually the first thing I do in this game as soon as I have some money is to hire a scholar (and an instructor) so that (a) I don't have to put any skill points into Identify and (b) any character can use the skill. This makes play simpler, because I don't then have the hassle that I have in MM8, of swapping items around to get them into the back-pack of the character with the identify skill.
