Lots off confusion and personal opinion will come up when we we talk about the Plain windows server and Control panel based server specially when we use it as web-server. Lots of things need to be considered while we thinking on the topic.
But obviously the control panel base server are more user friendly and hassles work. and might be a quick way to handle it by paying some extra money on the control panel. You may be thinking of saving some cost on the management of the technical support or upgrade of the panel.
Although sometimes having control panel we need to keep depend on the control panel provider to keep updated the patches and the security bugs in other hand for plain server if the person who is handling it is bit technical and familiar with the windows server side functioning can tweak it according to the need and do the custom changes as and when needed also having the more and more custom setting leads to protect from the most of the hacker as hacker generally take advantage of the commonly used panel bugs and the applications comes on it.
There are some free control panel comes for windows server but its recommended to check the security and the frequent update on the bugs from the opensource provider. Keep the plain server allow you to keep modifying the things according to your requirements time to time. If you planing to keep the plain webserver for you website you need to make sure that all the require modules and the function are enabled from the IIS and also if you using it as DNS and email server at same time. Its more sensible to configure it in well manner so that it wont get loaded or buggy and will keep your server secure.
Keep the firewall Active on your windows server does help a lot but its recommended to close all the unnecessary port on the server and only open the require ports . Keep your self familiar with the windows Even-log and the Task monitoring tools. Disable the sharing and the directory permissions secure.
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