Matomo can be used with Nginx instead of Apache.
As Nginx doesn't recognize .htaccess (by default) it is important to use a proper nginx config that blocks access to e.g. tmp/.

Therefore I'd suggest detecting nginx during the installer and show a notice to the admin urging them to take a look at the Matomo nginx config.

One way to detect it would be using $_SERVER["SERVER_SOFTWARE"] which returns nginx/1.14.0 for me. While it isn't 100% accurate, it should be okay for a notice.