What exactly does uBlue do differently to Silverblue, which makes it easy to modify those parts?

Perhaps I should've been more precise/accurate. The images offered by uBlue are relatively vanilla but "batteries-included" images of Silverblue/Kinoite etc that include the essentials from RPM Fusion among others and ensure that your system continues to function optimally regardless of ongoing issues related to mesa/Nvidia or whatever. So by themselves, they don't do anything special necessarily in terms of modifiability except for having baked in functionality for receiving cosigned OCI images. Which is where the fun begins with the template provided by uBlue making it very easy to create your own custom cosigned OCI image that is modified to your liking and which is continuously pulled from whenever your system does a rpm-ostree update. As the changes don't happen at the client-level (read: your device), but instead before/during 'base-image initialization', one is able to apply changes to e.g the aforementioned /usr directory simply by creating those (modified or not) files in the github repo of their custom image. The linked template is far from exhaustive as one is able to customize it beyond that for which one could refer to the Bazzite or Bluefin images to see the possibilities.

Note that the template of uBlue is only possible because Silverblue/Kinoite etc supports it. So one is able to forego uBlue entirely and create their own image from scratch (as long as it satisifes some criteria). The beauty of (the template provided by) uBlue is that it enables every mortal to engage with that system as it has been made remarkably easy. Heck, I didn't have any prior experience with git or Containerfiles, but I was able to spin up my own image in like two hours or so.