When playing with restricted scales on chord mode, both the input key and the processed chord respond to the note restriction.
Now picture this: when chord mode is on, the processing applies the note restriction, while the note physically played on the keyboard is let free from it. In this case each semitone played (most of them) will produce a different scale-coherent chord.
So instead of
Played note
⬇️
Scale quantization
⬇️
Chord
⬇️
Scale quantization
I suggest
Played note
⬇️
Chord
⬇️
Scale quantization
The result is sensitively different, try these chains on a daw to check.