In some cases it works to create Smart Objects for the added parts, and then add smart filters that blur the layer and sharpen it subsequently. Maybe ads some posterising to make color gradations less smooth. Be sure to get the color grading good before applying filters.
10 years after the OP, I was suffering (and getting frustrated) from the same thing in Media Encoder 2019.
But I found a solution.
It’s not in the settings pane, but in the upper left corner: set ‘Source Scaling’ to ‘Scale to Fill’. That should do what you want.
In a world were even Animated Gif returned as a popular file format, there are still plenty of jobs where QT lossless is a perfect choice. 2D animations without gradients most of time don’t need 16bpc.
Plus the integrated alpha makes it ideal for prerendered elements. Why not support it? It’s nice and usefull, and there is no alternative that combines lossless compression and alpha channel. Prores4444 comes close, but is a bit overkill in a lot of situations.