I read if the amount is sent from an external wallet, you need to wait for 6 confirmations before the coins can be sold, does this mean there is there a variance to how much I will get?
Yes, the exchange rate moves and you may get less or more than you would have gotten had the trade executed immediately.
This situation exists for many companies who do commerce in multiple nations, though Bitcoin's exchange rate volatility exacerbates the problem.
If your selling prices have sufficient markup, the exchange rate risk should normally not be that significant and probably evens out over time between the times the rate goes up versus the times it goes down.
If there is a larger transaction or the need to lock in at the exact rate from when the sale occurred, API calls to handle hedge trading using a custom approach rather than autosale is one solution.