Emacs falsely recommends removal of explicitly installed packages - Why?

Question

I am encountering a peculiar issue with Emacs's package management system where it is falsely recommending the removal of packages that I have explicitly installed via package-install. One such example is the markdown-mode package.

I have installed the affected packages explicitly using M-x package-install, so they are not dependencies.

I am using Emacs's built-in package.el for package management.

This behaviour is consistent and affects packages that I want to keep.

The recommendation for removal occurs when I go to the list of packages (M-x list-packages) and press capital "U" to update packages. Emacs then prompts me to update the packages and recommends certain packages for removal, even though I want to keep them.

I have checked the usual scenarios such as package dependencies and made sure I am using the correct installation method. I am unable to identify why this is happening.

This thread provides a workaround but does not explain why the package is excluded or indicate that it is a problem that will be rectified:

How does package-autoremove decide which packages to remove?

Why is Emacs recommending the removal of these explicitly installed packages, and is this behaviour which I have observed for a long time going to be fixed?

Emacs Version: 30

Any insights or guidance on this issue would be greatly appreciated!