I don't believe they throttle the engines up or down much during the second stage burn. Fuel decreases ~linearly and thrust is relatively constant. Acceleration increases as fuel mass decreases.
No, second stage has 3 vacuum engines and 3 atmospheric engines, so they'll have to be able to throttle for the cutover.
They might, I'm not saying your wrong, I'm just saying that I cannot imagine how you would justify the added complexity of doing it that way.
Better fuel efficiency = more payload to orbit = plenty of justification for the extra complexity.
Admittedly gravity losses are more significant at the beginning when the booster/ship are ascending purely vertically than later in second stage flight which is mostly horizontal, but definitely still a factor.