You can use the min-phase filter whether TP is used as a transport or transport+DAC.
In the case of using the TP as a transport with min-phase filter enabled, the sound of your DAC will be influced (I think positively, unless your DAC already has a min-phase filter) by the filter and parameter you set.
The headfi article is a little old. I have since modified the sox function to adjust the DAC sound to my taste. Right now I have touch (with boulder PS) running the min-phase filter into Cary exciter and the combo sounds wonderful in my secondary system.
I am no longer using transporter for much of anything since I acquired Linn Klimax.