Yes, unfortunately we can only add your custom logo/header to pages we manage, such as the initial checkout page; PayPal provides no way to customize their final payment page. Note that the third-party cookie blocking issue would affect ALL sites that use PayPal Advanced with Layout C embedded in an iframe; that issue isn't just something peculiar to our own system.
As for the new Admin, we had some false starts and unforeseen setbacks in 2011, but about a year ago we hired an experienced new developer specifically to help out with the new Admin project and got a fresh start on that; we are very conservatively projecting it should be done by the end of this year, and optimistically projecting very much sooner if all goes to plan. Initially, we're just shooting for feature-equivalence with the current Admin, to keep the project scope focused and avoid feature creep that would only set things back even further, but once that's done, we'll be able to start modifying it as needed to support new features and functionality.