Is there a reason why you want to use both external calibration and an internal standard? I don't believe this is usual practice, i.e. you would typically use one or the other.
This is the common practice in my laboratory which I have adopted since I am an undergrad.
I would imagine that it is assumed that the efficiency of liquid-liquid extraction of ethyl indole-3-acetate and benzedioxole are constant or change proportionally to each other. Extrapolating yields from the ratio of area of the product to area of the internal standard would account for any loss in extraction if the prior assumption is true. Our calibration curve is also based on the ratio of product of known concentration to area of the internal standard (extracted from a water/ethanol solution to DCM). Internal standard amount for known standards and reactions to be quantified are constant, of course.
I am worried that the prior assumption isn't true, however, since 1,3-benzedioxole is structurally quite different to the indole derivative.