Everything that is placed in your document head with the jdoc:include has been explicitly loaded by something in the system (an extension trying to use a component with a JavaScript dependency to MooTools as an example). So yes, you need this otherwise you are missing a lot of things that extensions do (not just loading scripts and stylesheets, many extensions also set metadata in the head for things like social sharing or SEO purposes). If you need some control over what is actually getting spit out in the head element, you can write a plugin hooking into the `onBeforeCompileHead` event to make the changes you need, but this should be done with care.
Joomla core does not alter your base <html> tag. So you most likely have an extension mangling it. Possibly a plugin hooking into the `onAfterRender` event.