Nope, it's just a packaging change for *hotfix* packages. Which answers your other questions: hotfix packages have restrictions imposed on their packaging metadata in order to pass through the native "Update Your Kindle" checks.
MRPI packages can be more loosely packaged.
The rest of the packages (with the exception of USBNet, which I forgot for your specific case) haven't been respun, because they're not actually useful on newer devices.
Assuming you're using a KindleTool version built from master, you can repackage an existing (non hotfix) package with a combination of kindletool convert + kindletool create on the resulting tarball.
e.g.,
Code:
kindletool convert Update_usbnet_0.22.N_install_pw2_and_up.bin
kindletool create ota2 -X -d kindle5 Update_usbnet_0.22.N_install_pw2_and_up_converted.tar.gz Update_usbnet_respun.bin