Is there a way to disable system warning messages popups for some specific user (or for all users also) in Magento 2?
Create a new role here if you have not created already System->User Roles->Role Resources If you have already created it then do the following System->User Roles->Role Resources (tab) from Resource Access drop down under system folder tree find the Other Settings now you can see Notifications you may enable/disablehere save the role and assign this role for specific users.
You can use user-role specific handles from this module https://github.com/TheFrankman/magento2-customhandles (very handy anyway) and then remove the block via layout:
<referenceBlock name="notification.messages" remove="true"></referenceBlock>
Until a proper fix can be rolled out, I created a userscript to fix this problem using Tampermonkey. For those that do not know what Tampermonkey is, it is a userscript manager browser extension, that allows users to install scripts that make on-the-fly changes to web page content after or before the page is loaded in the browser.
The script will reduce the width of the systemMessageBlock and move it to the top left corner. When the systemMessageBlock is loaded, it will hover over any text or elements in that corner, but after 5 seconds it will fade away.
This is an easy quick fix and doesn't involve touching the Magento code.