A PhD by published work "from scratch" is just...a regular PhD, essentially. As above you should just directly apply to PhD programmes in that case.
I think especially these days a PhD by published work (in the usual sense i.e. after the work is published) almost non-existent; I think it used to happen back in the mid-late 20th century where the academia pipeline was less rigid (see e.g. Jane Goodall). But now it's more or less impossible to get involved in those academic circles unless you are already in them by doing a PhD etc, anyway - and I'm not really sure you could get published in any reputable (i.e. not vanity) journal if you aren't in an academic environment anyway to get your name attached to a paper by an established researcher and then hence go on to publish more with your name in a more prominent role in the paper until you are being published as the full author of the paper/first listed name.
The only major exceptions I can think of are academic clinicians (medical doctors/surgeons that is) who have their degree(s) and do a lot of research as part of their work, but due to the demands of their work aren't in a position to go off and do a PhD as a standalone thing (although even this is more or less supplanted by the MD (Research) qualification in the UK which is essentially a PhD by published work with a slightly different name), or people working in R&D (mostly engineers I imagine) who likewise are already doing research and publishing as part of their job anyway.
They aren't then "planning" for the PhD by published work but just have done the work so why not send it off to get a degree to boot...