Guess I misread it. I thought the apply to all pages referred to the locking feature, but on second looks your explanation makes more sense.
One thing I notice, guides are not pinned to a layer. On my other Publisher, I could define guides on different master page layers and select by hide/show layer later. No problem, just create extra master pages. Another nice feature in Scribus is you can change your mind later as to which master page you assign. Couldn't do this with my other Publisher, had to add/delete page. My other Publisher for years has been PagePlus. Gonna miss it after all this time!!