Please please please don't write walls of texts in bug reports or feature requests. Write a concise description of what you want to do or what doesn't work. The back story is absolutely unnecessary in almost all cases and only makes it much harder to parse what you actually want. I tried to read through everything you wrote twice and I still have no idea what is actually the bug you are experiencing.

Ok... I will try my best to be concise and precise here...
Assigning MIDI notes to keyboard commands works for all velocities, so if I hit G-6 at velocity 5 it is the same as hitting G-6 at velocity 126 (I think that is the highest midi keyboard velocity)
I suggest when keyboard commands are assigned to a midi note input they only work for the highest velocity.
I assigned my mute button (F-10) to 'mute channel on transition' keyboard command, and the brackets that show the channel will change mute status only stay on while I hold the mute button down.

I will post some more information of how these midi keyboard button presses look on MIDI-OX and MIDIKey2Key in a few minutes to give you more information that I think will help in a few minutes.

Okay, so from my understanding there isn't a bug but the MIDI to keyboard shortcut functionality just doesn't work exactly the way you imagine it to work... The problem with generally restricting MIDI key pressed to full velocity is that this will not work with all MIDI devices. While it may be easy with your Launchpad to reach full velocity for a note, it is outright impossible on some devices (e.g. the Yamaha DX7 only has a MIDI velocity range of 0 to 100, if I remember correctly). So outright rejecting such MIDI messages cannot work as a general solution in OpenMPT.

PLAY/PAUSE button
Midi OX (timestamp ignored)
IN PORT STATUS DATA1 DATA2 CHAN NOTE EVENT
1 2 90 5B 7F 1 G 6 Note On
1 2 90 5B 00 1 G 6 Note Off
MIDIKey2Key
DATA | STS | CMD | CH | DATA1 | DATA2 | DESCRIPTION
805B7F| 80 | 80 | 01 | 5B | 7F | NoteOf G7 Velo=127
905B7F| 90 | 90 | 01 | 5B | 7F | NoteOn G7 Velo=127

MUTE button
Midi OX (timestamp ignored)
IN PORT STATUS DATA1 DATA2 CHAN NOTE EVENT
1 2 90 55 7F 1 C#6 Note On
1 2 90 55 00 1 C#6 Note Off
MIDIKey2Key
DATA | STS | CMD | CH | DATA1 | DATA2 | DESCRIPTION
80557F| 80 | 80 | 01 | 55 | 7F | NoteOf C#7 Velo=127
90557F| 90 | 90 | 01 | 55 | 7F | NoteOn C#7 Velo=127

I am including this (and it took a while to type out by hand) because I think this is information you can use... I am not sure what most of it means most of the time

"The problem with generally restricting MIDI key pressed to full velocity is that this will not work with all MIDI devices"
ok I see... so maybe another solution would be to set the velocity range?

Maybe. But it would add a lot of complexity and it's unlikely to happen very soon.

OK thank you :) I am sure I will find ways to make what I have work anyways... I was thinking of assigning some other keys to set modplug's octaves instead of using my octave buttons then I might get the result I am looking for, thank you for including this feature dude... I will just have to think a bit different to get it to work to my advantage. and merry xmas :)

ok now my play/pause seems to be g7... this is so very confusing... also I tried changing modplug's octaves and the g7 on the keyboard still triggered play/pause... and I assigned the play/pause button on the keyboard to play/pause in ompt... it plays as long as I hold the play/pause or g7 button down then it pauses... unlike the traditional F5 keyboard shortcut which plays until you press F5 again... it is just very strange... midi keyboards man..love them and hate them XD
sorry I am trying to make this make sense but it doesnt make sense to me...

anyways... I definately think this feature is a good step in the right direction for customising our midi keyboards' functionality in modplug, congratulations guys... :) unfortunately it doesnt seem to be a way for me to solve my problems without reaching into other software. the 'bugs' I mention above is the deal breaker for me... if I cant keep the keyboard functioning as usual and if I cant keep it playing the f5 way or mute/unmute a channel properly by hitting the button then this is unfortunately not what I am looking for... thank you very much for trying Saga and I hope you and everyone else have a good xmas.