Dear Daniel,
The natural frequencies presented in Table 9-1 of the NREL 5-MW specifications report (nrel.gov/docs/fy09osti/38060.pdf) were derived for a stationary rotor with a locked generator (RotSpeed = 0, GenDOF = False). Results for varying rotor speed and a free generator are presented in the following forum topic: Campbell diagram for 5MW turbine rotor.
Yes, the blade and tower mode shapes specified within the structural model of FAST v7 and the ElastoDyn module of FAST v8 are specified in a cantilevered condition i.e. the slope (coefficient of x^1) and intercept (coefficient of x^0) are assumed to be zero.
Yes, the coupling between the blades, tower, and drivetrain are considered within a FAST linearization analysis (depending on which structural DOFs have been enabled).
Best regards,