Magento 2.0.3 Fresh Install – Unable to Change to Developer Mode

Did you download version 1.0.0-beta from the releases page (or master branch), or off of the current develop branch?

My understanding is that the develop branch is not stable/sample data won't work, but it should be fine if you're using the official beta1 release. You can find that here: https://github.com/magento/magento2/releases

Both .phtml and .html files are part of the view layer in Magento 2 difference being phtml files work with Block which according to Magento Docs is a special PHP class that is usually (but not always) connected to a template closely. Blocks usually work with model layer (core Magento) to manipulate data and return results/response to templates (.phtml or .html files). These files are used by layout files in setting up templates for certain blocks and so on.

html files on the other end are solely used to display content on the frontend and javascript libraries such as knockout JS use them accordingly. These files are also used for AJAX content loading.