I guess I should clarify... its "per instrument per song"... so if you had 4 guitar tracks that would be considered 4 instruments... add a bass, 5 instruments.
Once the mix [rough balance] is going and the tracks are routed to the lines to the amplifier it takes the same amount of time to do each track... so if it takes an hour to get "track one" of guitar right it'll probably take at least an hour to get "track two" right... unless you wanted each track to have the same sound [not recommended... that will make the song a real bitch to mix].
From our perspective it would be like setting up for an overdub 4 times [4 different amps, 4 different mics, 4 different pre-amps, etc.]... and just as if it were an overdub session we'd still have to get all the sounds to work together in context [don't forget, we have our name and reputation to maintain!!!]. In the past we've done things like adding "far" mics and recording "ambience" tracks of the guitar in the room [no additional charge].
The client is more than welcome to attend the session [in fact, it is encouraged as we get instant feedback about what the client wants].
Peace.