Rather than trying to answer your questions individually, let me describe my workflow and see if it it helps you in any way.
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Create a new Studio One song using the blank template.
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Add Scaler, chord (e.g. Piano) and melody (e.g. Guitar) tracks using whatever instruments you want.
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Set the inputs of both your instrument tracks to Scaler 2.
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In Scaler, select a scale and create a chord progression (pattern) in section C.
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Set the Scaler instrument (it defaults to Felt Piano) to off.
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Arm Scaler and your chord instrument tracks for monitoring and recording.
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In Scaler, bind section C to your keyboard. When you play the chords, it will sound only in your chord instrument as the scaler instrument is off.
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Record your chord progression. It will record on your scaler and chord track.
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If you wish, at this point you can extract your chord instrument track (not the Scaler track) to the chord track in Studio One.
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Switch off monitor and record from your chord instrument track and switch off record from the Scaler track. Switch on record and monitor in your melody instrument track.
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In Scaler, turn on Keys Lock, select Chord Notes in the dropdown. In settings set Keys-Lock → Chord Mute to Muted (you can leave this on all the time, it only has any effect when keys lock is on). Before playing the song, test that you are only hearing the melody and not the chords. Note that you can only use the notes that are underlined in green on the Scaler keyboard in section A (the ones with numbers rather than note names (letters) on them. I set my keyboard an octave higher so I’m not playing at the top end all the time.
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When you record now, you will hear the chords from your chord instrument track, and notes from your melody track as you play them on your keyboard. It will only record the notes on the melody track.