Indexable option when setting up multisite

When using new blog templates there's a checkbox that says "Allow search engines to index this site".

From what I gather reading the forums the new site will default to the templates search engine settings, meaning what is the point of that question does it do anything? I've tested it on my website creating two identical sites one with indexability and the other without and both robots.txt files are the same. Leading me to believe it is just using the templates settings.

So the question is does that question actually do anything? And if not is that a bug?

If you are curious here are the two sites I setup:
http://indexlove.ourrockymountainwedding.com/robots.txt (yes selected)
http://indexlove2.ourrockymountainwedding.com/robots.txt (no selected)

Thanks for the clarification.