I guess you are already aware, but just to be clear for other readers, this is normal and expected.
Only the release versions of the library are available from Library Manager. The version in Library Manager matches the content of the repository at the 1.4.4 tag:
https://github.com/PaulStoffregen/Encoder/tree/1.4.4
If you want to use a non-release version of the library, you must install it manually.
That issue was submitted 2023-09-17, prior to the introduction of support for the UNO R4 boards on 2025-01-04. Unfortunately the issue was not closed at the time of merging the pull request that resolved it.