Dear Gerrit,
Yes, it is the mass and inertia of the RNA that is resulting in a different level of damping in the response than what you input as a damping ratio. The tower damping ratios specified in FAST apply only to the isolated tower, in the absence of the platform or RNA. Effectively, the RNA changes the generalized mass of the tower-bending mode, dropping the natural frequency and requiring a higher level of damping to achieve an equivalent damping ratio when compared to an isolated tower without the RNA. The RNA also impacts the gravitational destiffening of the tower; this term tends to be small, but has more importance the higher the mass of the RNA.
In your case it sounds like doubling the damping ratio for the isolated tower will give the damping ratio you expect for the combined tower + RNA.
Best regards,