JoshNelson...the "Message (HTML)" field of the product's settings;
When you say that do you mean the templated email area?
No, this only pertains to thank-you page customization, not emails; the "Message (HTML)" field is on the final screen of the product's settings. We realize that field label is a bit confusing, as it pertains to page output rather than email message customization, so the new Seller Admin we're building will relabel that field as "Product Thank-you Page HTML".
Using other payment services would not change the first two technicalities I listed, but they would at least bypass the click-through/timing related aspects in the final "For PayPal orders" technicality when the buyer pays directly with a credit card, in which case the payment processor notifies us of successful payment and redirects the buyer automatically. Note that PayPal Payments Advanced/Pro would still include a standard PayPal account-based checkout option, so buyers who pay with their PayPal account would still be subject to that last technicality.
To mitigate the "only item" technicality, you might consider using Buy Now buttons which bypass our shopping cart to take the buyer directly to instant checkout for just one item at a time, though this also means that Buy Nows cannot use features that depend on the cart:
Another approach you might consider would be using a Common Thank-you Page URL, as we would redirect to that URL after the buyer finishes checkout (presuming PayPal buyers click to proceed past the end of checkout) regardless of which item(s) the buyer purchased and regardless of whether PayPal had completed their payment by that point. In this case, you can also use the template tag [%thankyou_link%] in any of your thank-you email message templates to insert a link that would redirect to your Common Thank-you Page URL.