Considering that was most of the motivation behind the bill, what exactly is the point of it now? What new protection to "religious liberty" are the fine, good-natured folk of the Hoosier State now afforded?
The clarification more or less says that you can't discriminate against LGBT's in cities/counties that have nondiscrimination ordinances that cover LGBT discrimination. You can still do it in locations that don't have these ordinances. You can also still discriminate for other reasons - such as the fact that the customer voted for Obama or is an athiest - as long as you claim you're doing it for religious reasons.