Settings within a VirtualHost container will, if allowed there in the first place, work only for the relevant domain. Have a look at /usr/local/apache/conf/httpd.conf.
You can also do plenty with local .htaccess files.
I don't think so. If you place a file with permissions 600 and ownership root:root in a user's home directory, that user will still be able to edit or delete the file.
I am sorry, MMarko, but sleddog is right. Your can delete a file even if you chagne its permission and ownership. The best way around this issue is to SSH as root/su and: chattr +i WHATEVER_FILE