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The order of transactions in a block doesn’t have an effect on the transaction charges or the block reward.
Due to this fact the miner can, if wanted, differ the order of transactions with none change to the coinbase transaction. The coinbase is at all times the primary transaction.
As you say, the order of leaves within the calculation of the Merkle root would naturally be the identical because the order of the transactions within the block.
So the charge payout/incentive has no affect on transaction ordering (excluding coinbase) and vice-versa: the transaction ordering has no impact on charge payout/incentive.
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