Standalone NGINX

[MRM]

We have noticed that activating standalone nginx on one domain causes issues in other domains:
Assuming we have domain1.com and domain2.com, we have noticed upon activating standalone NGINX for domain1.com, the following .htaccess rules are being ignored / not followed in domain2:

Example:

<IfModule mod_rewrite.c>
  RewriteEngine on
  RewriteRule ^(.*)\.php$ ok.php?id=$1 [QSA,L]
</IfModule>

ok.php:

<?php echo "OK";

We have a similar rule in our JTL-Shop.

Question 1: Am I wrong to assume activating standalone NGINX on domain1 should not cause this on domain2?

Question 2: This caused us additional confusion, as some simple rules were followed, like this one:

order deny,allow
deny from all
allow from 127.0.0.1

Shouldn't nginx totally ignore all .htaccesses?

Question 3: From here, I found this: https://docs.directadmin.com/webservices/nginx_apache/customizing-nginx-apache.html

|*if HAS_PER_DOMAIN_NGINX="yes"|
        <tr>
            <td>|LANG_NGINX_ONLY|</td>
            <td align=center><input type="checkbox" name="nginx" value="1" |NGINX_CHECKED|></td>
            <td>|LANG_NGINX_ONLY_DESC|</td>
        </tr>
|*endif|

Where can we set HAS_PER_DOMAIN_NGINX to NO?
I have tried: /usr/local/directadmin/data/users/myuser/user.conf
It appears to be the wrong place, we would like to disable this feature system wide.

Thank you for your time and we would appreciate your help.