Problem/Motivation
MessageCommand was introduced in #3086096: Add a generic Ajax Message command. It is helpful to show status messages in AJAX contexts. Sadly it uses a totally different "render pipeline" than the active theme does. In fact it uses none, but builds the message area in JavaScript, without using the Theme's twig templates. That's how it's implemented.
From a Themers and Theme Prespective and from "Component" thinking, this is wrong. AJAX messages should use the same templates, as regular messages do.
That's why I'd rate this as bug from outer perspective. Still I think it was a (discussable) design decision.
This results in issues like this: #3165452: Override Drupal.theme.message to to make sure JS messages get rendered correctly
Of course, I know talk is cheap and this is hard to resolve, because the messages are added dynamically and you can't tell if the message area already exists. But these problems can be solved.
Implementation:
https://git.drupalcode.org/project/drupal/-/blob/11.x/core/misc/message....
https://api.drupal.org/api/drupal/core%21lib%21Drupal%21Core%21Ajax%21Me...
The devel maintainer also points out that currentlydsm() / dpm() are broken and could be fixed in this issue: https://gitlab.com/drupalspoons/devel/-/issues/525#note_2039843855
Steps to reproduce
Show a regular status message using PHP in a custom theme, where the message area was modified in twig
Compare the result to a status message added by JavaScript. They differ a lot, if the JS-built dom structure isn't the same as the one in Twig.
Proposed resolution
Return the theme rendered message wrapper and the messages in the AJAX result. Only add the wrapper on the page, if none is present.
After adding or if the message wrapper is already existing, add the rendered messages.
This way the theme handles the message output, like it would do on a regular call, but AJAX builds the message from the theme results without a difference.