All intentional. The logo issue is probably down to needing to set a width for it as per the release notes: https://moodle.org/plugins/pluginversion.php?id=10845. When you updated you should have seen the new logo width setting as a part of the update process and had an opportunity to set it then.
RE: "when you scroll away the photo goes back to normal size, but the logo area stays shrunk." - umm when you scroll away you can't see the logo either, so how do you know it stays shrunk?
When I looked at the header with the old navbar position I thought, what a waste of space. So I thought I'd make use of it with a new feature that happens only on desktops and only when at the top. Ok, no setting to turn it off yet as I did not anticipate it being disliked. I thought it would be a good improvement to evolve the theme in a modern direction. Evolution does not stand still, stagnation is death, change does bring fear but it also brings new opportunities.