Basically when installing the commerce kickstart at least at around commerce_kickstart-7.x-2.37-core; At the "Configure Store" Page under Functionality, you have two options. Yes "(Shows you everythingCommerce Kickstart can do........". s. And No option.

If you select yes. You will not have the issue I mentioned above.
However, if you select No, then, you will get the issue I mentioned above.

As is with the latest version of Commerce Kickstart 2 the Fancy Attributes Module comes installed an enabled. And it turns out it is enabling this modules that will automatically give you the “Add to Cart form – Attribute” mode in the Manage Display when you add The field on the Color Vocabulary. So, as a work around, go ahead and disable the Fancy Attributes Module, Save. Then enable it again, then Save. At this time you should see the “Add to Cart form – Attribute” Mode, and the “Rendered form” under The “Enable this field to function as an attribute field on Add to Cart form”. This is a work around. I am new to Drupal and commerce kickstart. So, I am still trying to find out how we can make his issue not appear any more, and to share information in case someone else faces the same situation