bug#63891: 29.0.91; customize-save-variable should not save all variables if a custom file exists

[Jimmy Yuen Ho Wong <wyuenho@gmail.com>]

As a discussion from bug #63300, it appears this long standing
undocumented behavior of `custom-save-variable` is coming into conflict
with the introduction of `connection-local-*` variables being user
customizable and the fact that Tramp in Emacs 29 sets them on
load. Here's a scenario where the combination of these behaviors results
in one too many surprises:

0. (setf custom-file "~/.emacs.d/custom.el")
1. M-x load-library tramp (or install a package that transitively
requires tramp, without the user knowning)
2. Now `connection-local-profile-alist` and
`connection-local-criteria-alist` are set by
`hack-connection-local-variables-apply`.
3. M-x list-packages
4. Installs a new package
5. Now in addition to `package-selected-packages` being updated, 2
gigantic variables are also saved. Since these connection-local
variables are highly machine, application and connection dependent,
saving them into the custom file will make it very annoying to be shared
across multiple machines. This violates the principle of least
astonishment.

Expectation:

`custom-save-variable` should only save the value of one variable
regardless of whether a custom file exists.