Actually, I take it back. customize-save-variable only saves variables that have the saved-value symbol property set. This property is normally set by customize when it is saved to the custom file. Something in Tramp is setting this property without saving the variable values to the custom file or going through customize. In fact, you can see it via M-x customize-option connection-local-criteria-alist. The value will be shown as SAVED.
In addition, setting `enable-connection-local-variables` to nil early in early-init.el has no effect, the variable is still set on load.
Both of this behavior violate what is documented in the docstring and https://www.gnu.org/software/emacs/manual/html_node/elisp/Standard-Properties.html.
If you must, enable-conneciton-local-variables should be respected, and if you must, set the theme-value property on these connection-local variables instead of saved-value so custom-save-all will not save them.