So...
1. A gay couple walks into a baker to order a wedding cake, the law provides the baker can use religion as a means to refuse service.
2. Two weeks later the baker and his wife walk into a antique shop owned by the gay couple and the gay couple refuses to serve the baker because of the bakers religions beliefs.
In event #1 the baker will be exempt from Public Accommodation laws because he acted on his religious beliefs,
You are misstating the law. It does
not "provide the baker can use religion as a means to refuse service." It does
not necessarily mean the baker in your first example "will be exempt" from the applicable public accommodations law. State RFRA's like Indiana's do not, by themselves, excuse private persons from complying with laws that burden their religious beliefs. They allow them
to raise that issue in their defense if they are sued, but they will still lose the suit if the court doesn't buy that defense.
The RFRA's usually also require government, when it burdens religious expression, to show it has a compelling purpose for doing that and that it is doing it in the least burdensome way. Put differently, these laws require government actions that burden religious expression to meet a "strict scrutiny" standard similar to the one the Supreme Court required them to meet in its decisions before 1990.
on the other hand the gay couple would be charged under the Public Accommodation law (if sexual orientation is covered by that State's law) and the complaint would proceed. They of course being in violation of both State and Federal law.
I don't understand that. In your second example, whether sexual orientation were a protected category in the state public accommodations law would be irrelevant--the people being denied service are being denied because of their religion. Whether the owners of the antique shop who are denying service are homosexual does not matter.
States can and have added more protected categories to their public accommodations laws than are protected under federal law. And states have inherent authority to do that. But the further they go in this process, and the further they expand the definition of public accommodation, the more likely it becomes that these laws will violate the Constitution in some way.
Discussions on this topic help reveal ersatz liberals for what they really are--which is the very opposite of liberal. True liberals strongly defend the First Amendment freedoms of religion, speech, and association. Ersatz liberals view these freedoms as obstacles to the social agendas they want to ram down everyone's throat. They are in fact the very kind of intolerant, self-righteous prig they are so ready to accuse people who do not share their views on subjects like homosexuality of being.