Well, yes, I consider this a poorly considered “feature”, or arguably a bug, for exactly the reason you said, they are local to connections and machines, and thus highly variable.

We can probably argue whether this is a bug in tramp or a bug in customize-save-variable tho (why on earth does the act of saving a single variable value saves all customized values if a custom file exists?)

On 4 Jun 2023 at 1:05 PM +0100, Michael Albinus <michael.albinus@gmx.de>, wrote:
> Jimmy Wong <wyuenho@gmail.com> writes:
>
> > Again, I think if tramp needs to cache the values of these variables,
> > they should be written to a file in user-emacs-directory, not hacked
> > in a customizable variable.
>
> But these Tramp settings are connection-local, meaning they are
> different for different remote hosts. Connection-local variables have
> been invented for exact this purpose.
>
> Now we can argue whether connection-local-*-alist shall be user options
> or not. But exactly this has been requested, and that's why they have
> been adapted. Your request is the opposite ...
>
> Best regards, Michael.