1. 2-layer flex vs 6-layer rigid-flex? 2 layer flex is fine.
2. add top ground hatching at the expense of smaller sensor size? Since no enough space to place ground hatch on top layer, ground hatching can be cancelled i think, but you must consider ESD problem of sensor. I recommend you not only series a 560 ohm R on sensor line, but also plus a 10pf cap between sensor pin and ground(cap must be placed near to sensor pin). In that way, we will get a RC low-pass filter on each sensor line.
3. smaller buttons with increased spacing or larger buttons with minimal spacing? I recommend you increase spacing for independent button, 1.38mm is too less. I recommend you use rounded-square buttons, spacing between the buttons increase to 2mm.
4. rounded-square buttons to achieve maximum sensor area or circular buttons? rounded-square buttons
5. for the swipe sensor, is the chevron shape preferred even if I don't care about centroid? Chevron shape is prefer.
Note：The bottom layer of the FPC can be laid with a very sparse ground grid (like 10% filling gnd hatch) or just blank. Do not lay solid GND floor or dense ground hatch, it decrease sensitivity of the sensor.