There is definitely an issue with how Elements is publishing (or not as the case may be). I updated a PHP file in shared/assets and when I published the site, it wasn’t updated.
So I did a publish all and that didn’t update it. I then quit Elements and then restarted Elements and did a Publish All (having deleted all the files on the published site) and then it was updated. However, that process caused another issue as not all the backend RW folders were created with their content.
From my PHP log (edited):
[28-Mar-2025 18:42:12 UTC] $backend_path: ./backend/rw6BBC91D5_50AA_44A1_AED3_2FE25FF7EF79/
[28-Mar-2025 18:42:12 UTC] $site_asset_path: ../rw/elements
...
[28-Mar-2025 18:42:12 UTC] PHP Warning: require_once(./backend/rw6BBC91D5_50AA_44A1_AED3_2FE25FF7EF79/Parsedown.php): Failed to open stream: No such file or directory
PHP is correct, it isn’t there. I would expect three of these type of sub-folders to be present but only one is. 
At the moment, quitting Elements, restarting and republishing isn’t resolving the issue.