Hi,
Regarding Q1 - You will have free access to MCE seats from the time of booking.
Q3 - POUGs are only offered to bookings on BA.COM in my experience, though I was once able to POUG a telephone booking, but it had BA flight numbers and was point-point booking. So no POUG if booked through AA.
Q2- If it's a BA flight you are booking through AA, you will be able to link it back to BA. If it's AA flight, booked through AA, I don't know.