You are not charged twice. However, you are charged
* final value fees (in your etsy bill) for any transaction regardless of how it is paid
* with payment via direct checkout you pay a payment processing fee the same as you would via paypal. This is deducted from the total and shows in your shop payment account. I don't recall the precise numbers of one vs the other but they are essentially the same - on some I note a penny or 2 difference.