No oficial response, but looking back on older questions I found this one: https://wordpress.org/support/topic/hardening-wordpress-nonce-verification-failed?replies=10
In there the dev says to go to the plugin Settings -> Scanner Settings -> Scan error log files -> Disable
That fixed my 404, will check all my other websites that are giving the same 404 and will mark this as resolved in case this works. Not ideal, but works.
Disabling the error logs scanner does not affects the security of your site, actually that scanner is intended to be used by web developers temporarily while they are making constant changes in the production servers where their sites are running.
Another solution could be to ignore some of the directories that you think may not be necessary to scan, you can do this using the “Ignore Scanning” tool located in the plugin’ settings page. This will force the plugin to skip the selected folders during the file system scans.
Since the performance of the code is heavily tied to the configuration of the PHP interpreter on the server where your website is hosted, I can not do much to solve this issue unless I force an increase of the memory limit and/or the maximum execution time of the PHP scripts, which will lead to other problems. So I will keep this simple.
You can keep the error logs scanner disabled while you are not using the administrator panel, and enable it when you need to check if there are errors associated with the code of your site.
