$100 is the transaction value,it is not the cost of the transaction fees.

The fee is $1. They charge a 1% fee for instant payouts.

You don't. They are accepting $100 worth of BTC, converting it to dollars and giving you the dollars. They are basically operating like a credit card processor with a 1% fee, allowing you to accept bitcoin but operate in dollars.

It sounds like the fee is about $1.00: the delta between $100 and $99.

??

The merchant requests 100 USD. The user pays X BTC equivalent to 100 USD. The merchant receives 99 USD aka the fee is 1 USD