I agree, which is precisely why the fades are there. In each case, I feel the type and length of the fade is adequate. Granted, it is possible that I have watched this footage too often and that I am missing the novelty of the edit--or maybe you were watching with some biases that impacted your initial perceptions. We'll see what happens when more people watch.
I am reasonable. If dozens of people have the same impression or interpretation that something isn't working, then I will re-visit the material and try to (a) appreciate the problem myself, and (b) devise a creative solution.
Regarding each instance...
In the first case, Yoda (and company) have already entered local airspace by the time the scene ends (even in the original footage), and so a blend fade is used to get from the ship to the surface. We need only account for the landing. It is not specified where the temple is located, but it seems that the congress hall and temple are situated in the same part of the city.
In the second case, a fade to black is used because we do need to account for a longer passage of time. I am fairly confident that THIS particular transition works, partly because the second sequence is itself delayed (even after the fade is completed). Each time I watch this sequence, I have the sense of a chapter change--and that is exactly what I was going for.
Enjoy the rest of the material as it comes out.