I use Priority Mail flat rate envelopes and boxes for the majority of my eBay shipping needs (domestic and international). In situations where I think the pricing will be lower by using an alternative Priority box, I take that route to save money.
As a seller, sometimes I “guess” what I think shipping costs will be for larger items…but I never make my buyer pay extra. If the actual shipping price is lower, I issue the difference back via PayPal.
Never make your customers feel you are taking advantage of them. Nothing infuriates me more than being overcharged for shipping! If I was incorrect with my guestimate and shipping costs are more, then I eat the costs.