I have answered your post about
[LegacyDisable](https://superuser.com/questions/1183842/in-the-windows-registry-what-is-the-legacydisable-string-value-and-what-exact)
and have some knowledge of the subject.
As this post does not have answers, I'll try, although my answer may not be
satisfactory.

The problem with these registry items is that they are undocumented.
Each new version of Windows may add some more or invalidate others.
Since they are undocumented, Microsoft keeps the freedom of freely modifying
whatever it likes,
so the burden of verifying whether they still work or not falls on the users.

Information about these items comes from Microsoft in all sort of unofficial
channels. Sometimes they are found in SDK samples or on the MSDN,
sometimes in forum answers by Microsoft engineers,
and sometimes from clients of Microsoft that had privileged
access to Microsoft engineers.

I have found one person who has compiled a list of all known such items
in the article
[File Type Registration](https://windowssucks.wordpress.com/file-type-registration/),
each with explanation and a link to documentation.
Not too surprising, most of the items don't have documentation links.

As regarding `ProgrammaticAccessOnly`, this article only says
"Removes verb from IContextMenu enumeration?", but has no documentation link.

Searching via google, i have found a
[Winaero article](http://winaero.com/blog/how-to-remove-bitlocker-from-context-menu-in-windows-10/)
that says:

> ProgrammaticAccessOnly does the main trick. It is a special parameter
> which tells the Windows Explorer shell that the context menu item can
> only be accessed by software programmatically. The user interface gets
> locked down, so the command disappears from the context menu!

Together, it seems that these special registry items are recognized by the 
[IContextMenu interface](https://msdn.microsoft.com/en-us/library/windows/desktop/bb776095%28v=vs.85%29.aspx?f=255&MSPPError=-2147217396),
defined as :

> Exposes methods that either create or merge a shortcut menu associated
> with a Shell object.

The IContextMenu interface is exported by Shell extension handlers,
chiefly used by Windows Explorer.

In summary, the presence of `ProgrammaticAccessOnly` causes the shell
enumeration to ignore the shell item, but programs can still refer to and update
them via the IContextMenu interface or directly by modifying the registry.