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There were a couple of questions there:

Yes, exterior shading surfaces (site or building) will have the desired effect of reducing the PV output when they cast shadows. You need to ensure that your selected solar shading model is accurate enough for the job.

If you use a shading surface as a PV panel, yes the default is to make the entire polygon PV area. You can use a shading schedule to reduce the total area to that of just PV, i.e. a BIPV window that only has, say, 50% of the window area covered in PV. You'd set your "schedule" to 50% shading, 100% of the time. There is an OpenStudio measure here that follows the shading surface + shading schedule logic for creating such a system.