The order of transactions in a block does not affect the transaction fees or the block reward.
Therefore the miner can, if needed, vary the order of transactions without any change to the coinbase transaction. The coinbase is always the first transaction.
As you say, the order of leaves in the calculation of the Merkle root would naturally be the same as the order of the transactions in the block.
So the fee payout/incentive has no influence on transaction ordering (excluding coinbase) and vice-versa: the transaction ordering has no effect on fee payout/incentive.
