I’m having the same type of problem.
WP installed in public_html/
PHPList is in public_html/lists/
To install phplist I need to run https://www.mysite.com/lists/admin
This brings the 404 error from WP
public_html/.htacess contains
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
So I tried a number of things to try stop it.
including
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} -d [OR]
RewriteCond %{REQUEST_FILENAME} -f
RewriteRule .* – [L]
Still cant run install scripts on any other directories that are not WP.
Any ideas?