the first method will work fine for direct play medleys, where you want to mute the melody and play any conductor voice of your choice instead. If you want to use panel memories for the conductor voices just turn off part 1-16, tempo, etc etc down the list in the filter to stop these changing the things you don't want changed in the midi file.

If you want to change voices on the fly in direct play or from sequencer, use the mixer.

If you want to save midis with banks of panel memories preprogrammed with either sound changes in the midi tracks, or with preprogrammed conductor voices independent of the midi tracks this can be done too, it all depends on specifying what you want to do.

the simplest example:

initialise.
load midi.
save panel mem 1.
play the midi and change the lead voice in the mixer.
save pan mem 2.
stop, sequencer reset, press pan mem 1.
save technics sequencer, pan mem and current panel only.

initialise again (to prove it works).
load your midi and play it.
any time you want to change to your pre-programmed alternative melody voice just press pan mem 2.

if you want to include conductor parts, then follow a combination of the two methods. If you want to use conductor parts from panel memory but leave the midi backings unchanged
this can also be done. The exact method depends on whether you want to direct play, or medley from the sequencer.

It is feasible to change all 16 parts of the midi from panel memory, your idea of a blanket setup would not work for many midi files, because you don't know what you are changing to what - you can't change piano with sustain pedal to trombone for instance - you need to choose your instruments for each song, or sort banks of songs with compatible orchestrations for each track.