So here I'm going to try to clear up the mess about how bitcoin futures exchanges calculate fees and how it all works by focusing on four key concepts:
1. Maker/taker incentives: Most exchanges have a maker/taker fee model. This means that they charge you one fee for when you put or "make" a limit order in the orderbook, and they charge you a different fee for when you fill or "take" a limit order. Why do bitcoin exchanges charge different fees for different trading? Because they want to encourage liquidity. By charging a lower fee for maker orders, they encourage traders to put orders in the orderbook, which makes the exchange more liquid in general for other traders to get involved. BitMEX is a good example of a bitcoin futures exchange that offers this. They even have a rebate (negative fee) for those who provide liquidity with maker limit orders.
2. Volume incentives: Some exchanges offer a sliding fee schedule based on volume, which rewards traders with lower fees if they have a certain amount of volume over a period of time trading with the exchange. This is to incentivize traders to be more active and encourage them to reach higher tiers of contracts traded in order to graduate to lower fee levels. CryptoFacilities has this exact system, where they offer to cut fees from 0.03% to 0.01% for liquidity providers who satisfy a certain amount of bitcoin moved over a month period.
3. Open/close distinction:There's also a distinction sometimes between opening a position and closing a position. One "trade" constitutes opening and closing of a contract position. OKCoin for example charges one fee for opening a position and nothing for closing. This is because they don't need to attract liquidity as they are the market leader in bitcoin futures.
4. Fee as % of notional value vs. initial margin - Finally, the issue of leverage. All the exchanges charge the fees based on the notional value of the contract. Different exchanges allow for different amounts of margin to be put down for trading at various levels of leverage, but this does NOT affect the fee you're paying on the amount the contract is worth. It technically effects the fee you are paying as % of your margin, but it is a strange distinction to make. Obviously at 100x the fee as a % of the initial margin is going to be higher than an exchange with 5x maximum.
Below is a table comparing the main bitcoin exchanges OKCoin, BitMEX, and CryptoFacilities fee types, for your convenience: