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welcome back :)

Automation and midi CC
automation and midi controller assignment (aka. midi learn) are two distinct feature functions that just happen to have the same item subjects (eg. plugin parameters); but if you select automation for an item that is also assigned to some midi controller then you can record (live) all the midi controller gestures into the automation curve--the automation data points are just added on-the-fly while you turn the controller knob (or slider) or even if the controller events are produced by another sequencer, application or elsewhere.

Background sequence
nope. this is certainly a feature request for the midi clip editor i guess.

Key and Scale
the key/scale are just entry input filters like snap-to-grid (which now turns as snap-to-scale) when entering, editing or moving up or down selected note events; perhaps to change existing selected events into a given key/scale is what (from menu) Tools/Quantize/Key, Scale does instead.

hth.
cheers