Hi Andrei,
It would be possible to add an option like this (suppress note on/off) but the results may not work as expected. There are a couple reasons:
1. When the software receives a note on message, it first sets up the default values of certain controllers (e.g. pitch wheel and whatever other ones are being controlled from the TouchKeys) before it sends out the note on to the synth. Using the synth's built-in note on and ignoring the one from TouchKeys, it is possible that there might be some glitches at the beginnings of the notes. It depends on the implementation of the synth. However, if you don't hear any glitches on your synth then I guess it's okay.
2. For independently controlling several notes at once, the TouchKeys software has a "polyphonic mode" which allocates each note to a different MIDI channel. That means that the Note On message comes back in on a different channel than it came from the keyboard. If you suppress Note On messages from the software, that mode won't work anymore.
If neither of these is a problem, and there are no other solutions, then this could be an option. It's surprising that local control can't be turned off! Usually disconnecting the internal keyboard from the synth without disconnecting it from the MIDI output is an option that most synths have. But each one is different and I've seen a few surprising setups.
Another idea would be to try to set the internal keyboard to a different MIDI channel than the one your synth responds to (if this is possible). For example, could you have the keyboard send on MIDI channel 16 but not have the synth respond on that channel? Then the TK software could send the messages back on a different set of channels, and you would avoid a loopback.
Also, make sure that any kind of local echo is turned off on the synth or you will definitely end up with a MIDI loop!
Let me know how it goes.
Best wishes,
Andrew