I think I understand what you mean but in that case I would just remove the midi connection from the matrix to the mini and then you can still process the audio from the mini but be able to play it freely. The TRS insert connection (I think that's what you're referring to) is typically used for external effects to be inserted after the amp section of the audio path, if that makes sense.
If you are wanting to slave the mini to the clock of the matrix then i would try using the 1/8 inch SYNC OUT from the matrix to the CLOCK IN of the mini. I hope this helps.