I have been told by people at PayPal that there is no issue with having multiple accounts for this purpose, and by someone high up in the digital products division that they are working on unifying the process. (In fact, I believe they already are with the new adaptive payments flow, but I haven't had time to look into it yet. I am totally willing to believe that they haven't gotten to it yet.)
On that note, however, if you are doing US transactions, Amazon Flexible Payments is amazing: the fees are, again, worst case, the Stripe fees, but they automatically select the payment bracket that makes the most sense for the transaction at hand; they can scale transactions down to fractions of a cent.
More importantly, with Amazon Flexible Payments, they charge you a different amount of money depending on how the money was transferred: their risk profile is different for credit cards, bank transfers, and account-to-account movement, and they expose this directly to you, decreasing the costs for less risky transactions.
(Of course, unlike PayPal and Stripe, Flexible Payments isn't quite as integrated a solution: they do not support things like card-present transactions, for example, and require all purchases to go through their payment flow.)
On that note, however, if you are doing US transactions, Amazon Flexible Payments is amazing: the fees are, again, worst case, the Stripe fees, but they automatically select the payment bracket that makes the most sense for the transaction at hand; they can scale transactions down to fractions of a cent.
More importantly, with Amazon Flexible Payments, they charge you a different amount of money depending on how the money was transferred: their risk profile is different for credit cards, bank transfers, and account-to-account movement, and they expose this directly to you, decreasing the costs for less risky transactions.
(Of course, unlike PayPal and Stripe, Flexible Payments isn't quite as integrated a solution: they do not support things like card-present transactions, for example, and require all purchases to go through their payment flow.)