Syncthing Tray refrains from doing modifications to your Syncthing instance regardless whether it is local or remote. Only if you explicitly trigger an action that would cause a config change (e.g. pausing a folder) it will modify the config (again regardless whether it is local or remote).

You probably want to skip the setup wizard completely, though. It will not be able to configure connections to a remote instance. You just have to fill out the connection settings manually.

Note that the wizard will override any existing connection configuration of Syncthing Tray itself (e.g. to a remote instance) but it'll keep a backup of the overridden config as secondary config (visible in the combo box in the connection settings). This remark is only about the configuration of Syncthing Tray - as state before no config changes to your Syncthing instance are done.