Re: Acoustic pickups
You are right about the reason why our instrument sounds boxy, though the Radius is not a microphone transducer, but a piezoelectric transducer. As such it reacts to the Body's movements at the point of contact and is therefore lacking in the high frequencies you are used to hearing from your instrument acoustically. This results in what you are calling boxy.
Generally the reason people plug the f-holes to dampen the resonant frequencies of the body, and in turn aid in achieve more gain before feedback.
A parametric EQ can aid in both notching out problem feedback frequencies or trying to boost what you think is lacking.
Something like an AKG 411 might be a more balanced tone, it still relies on contact (and would be helped with an EQ etc), though being a contact condenser mic should sound more natural than a piezo pickup. I have used it on 'cello and it sounded great, and certainly there are folk here that swear by it for mandolin.
Hereby & forthwith, any instrument with an odd number of strings shall be considered broken. With regard to mix levels, usually the best approach is treating the mandolin the same as a cowbell.