As I saw (see comment) GM_registerMenuCommand is replaced with HTML5 context menu. and there's no plan to add it in GM 4.x.

Nevertheless, I've started this separate issue. in hope that you'll might reconsider.

I understand that adding some context menu options in the native context menu,
is useful for those that do want to add more entries in that.
Such as this new test script by arantius search-with-google.
screenshots:

But, for userscripts that use GM_registerMenuCommand only for settings, i.e. you only configure then only once in a while.
and apply to all pages,
such as the popular:
Mouseover Popup Image Viewer, (settings screenshot)
YouTube Link Title (settings screenshot) and
Linkify Plus Plus (settings screenshot )

Imagine having installed these scripts that create a total of 3 entries on top of the context menu
that are not needed most of the time:
it would make use the context menu on the page cluttered and unpractical.

And then the script author, in order to avoid cluttering the context menu just for the sake for offering settings,
he would either register a keyboard shortcut on every page (with no UI?)
or create a new dedicated button element on every page.

So, I'd like to ask you please to reconsider implementing GM_registerMenuCommand inside the toolbar button popup, similar to how it was in GM 3.x, as well as in the other most used scripts managers available, Tampermonkey and Violentmonkey.
,
It would appear between/below the "Greasemonkey is active/disabled" entry,
and above the 'User scripts for this tab' list (GM 4.1 beta4).