if you have a file at WP_CONTENT_DIR/install.php it will be run before the upgrade starts. If you want to override specific option then you can use the pre_update_option_$optionname filter to control the value written to the DB.
something like
add_filter('pre_update_option_admin_email','wpse_120475_myadminmail',10,2);
function wpse_120475_myadminmail($newemail,$oldemail) {
return '[email protected]';
}
caution – wasn’t tested but I assume that the filter API is available at that stage.
As for rewrite rules, the tricky part is generating the .htaccess file but since you obviously create your own installation image then you can add to it the .htaccess file in the root directory (the .htaccess is very generic and not tied to a specific domain name or directory location). Then all that is left to do is to control the rewrite rules options using the technique described above.
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