order Transactions within a block have no effect on transaction fees or block rewards.
Therefore, miners can change the order of transactions if necessary, without modifying Coinbase transactions. Coinbase is always the first transaction.
As you say, the order of the leaves in the calculation of the Merkle route is naturally the same as the order of transactions within the block.
Therefore, payment/incentives for fees do not affect trading orders (except Coinbase) and vice versa. Transactional orders do not affect payment/incentives of fees.
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