The '-q' argument on a php command is for the CLI (command line interface) version .. it tells PHP to not emit HTML headers.. just the print/echo outputs.
PHP CLI docs at
http://php.net/manual/en/features.commandline.options.php I find it useful to have a Windows Help version on my system.. you can download from
http://php.net/download-docs.php (I use the .chm version).
You may not be able to see .htaccess in your File Explorer in Windows if you have Hide Extensions turned on.
Yes, GoDaddy does have the setup of the filesystem different from other hosters.. they all have their own ways of doing user filesystem addressing. The $HOME shell variable always has the full filesystem path to your home directory. Some hosters have $HOME/public_html as the root for the webserver, others use $HOME/www or $HOME/httpdocs .. it varies from hoster to hoster.
Likewise, each hoster has their own placement for the PHP interpreter .. /usr/bin/php, /usr/local/bin/php, /usr/bin/php7 (etc) .. you have to find that out based on their docs or a quick call to their tech support. You won't be able to see any /usr/local/bin stuff via FTP as your FTP 'home' is likely fixed to $HOME. To see other directories, you'd have to use SSH to connect to the webserver itself, then a shell ls command to list other stuff (but you may not have permissions to see stuff outside your $HOME directory for security reasons). Using SSH, I find that (sometimes) a 'whereis php' will show the locations for the PHP interpreter (usually). The definitive answer should be obtainable from the tech support from your hoster.
Lastly, shell scripting (sh) used by cron is similar to (but not the same as) Windows DOS/batch files .. and, there are multiple shells sh, bash, tcsh, csh available on multiple platforms.. each with a similar language, but different. Generally, cron will use sh syntax/commands.