Thank you for sharing your thoughts.
All controls which use external templates are listed in the control configuration file part of the external templates archive file which you can download from your client account. Controls such as the search controls, and forum controls which do not use embedded templates can be configured from their control editor to use a different path for the control template, see attached image. So you can simply copy their templates to another location, edit them and then point the controls to them.
Files located in ~/Sitefinity/UserControls/ such as navigation and login controls are simple user .ascx controls with code behind file. WebUserControls do not support embedded templates. If you wish to modify them, but keep the original in the Sitefinity directory you can do is to copy/paste them to another location and then change their url property in your web.config file:
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