Just an FYI, but as I recall Ron has designs to implement last.fm (Audio Scrobbler) compatibility within mt-daapd at some point. Should this ever be realized, then your skip requirements may be problematic.
According to the last.fm submission framework, a given track must play, without break, for at least the first fifty percent of total play time in order to be counted. Subsequent to that threshold, one can scrub forward or backward as desired to repeat or otherwise manipulate the stream, yet maintain full credit.
It would seem to me that, in order to satisfy both your skip requirements and the submission protocol for last.fm would require a duplicate accounting routine — one to ensure that a skip not be logged as such locally unless such is done "within the first 1
(2?) minutes of playing the track" and another to ensure that no skipping whatsoever is executed for the initial half the track duration to satisfy last.fm credit requirements.
Unless you are listening to your music directly from the original media, it would seem to me a much more efficacious practice to edit the problematic tracks you cite in order to remove the silent portions. I, too, have around half a dozen or so tracks which have this dead space — either at the beginning or between the end of the music and the commencement of some "hidden" content. All have been edited to trim the dead air and, if necessary, generate a new track.