Right, private entities are not required to implement the bathroom portion of the law, but the rest of the legislation provides that NO local anti-discrimination ordinances/protection are valid.
So the hypothetical about apartment hunting, internships etc. are all valid. Discrimination because a person is LGBT is legal in NC, even if local jurisdictions want to provide otherwise. So, Durham, Raleigh etc. can’t just choose to be discrimination-free zones, because the State law says their laws banning LGBT discrimination are unenforceable. There is no remedy for LGBT discrimination, even if the local laws would otherwise allow it.
Back to the OP – who is trying to decide between the more affordable option of Grinnell – a highly regarded LAC – and Duke – a highly regarded private research university. The OP said they are concerned about not being swayed by prestige and reputation, are very concerned about finances, and want an LGBT-friendly community. Many of us said Grinnell is a great option, and that just because it is cheaper or in Iowa does not make it less desirable. As I noted earlier, the President of Grinnell is a gay man, married to his partner, with kids. Grinnell is one of the most diverse and tolerant LACs out there, with a $1.5 billion endowment which allows it to pour money into undergrad experiences and opportunities.
The OP has two (three, really, but Dartmouth seems to have fallen off their list) options, all of which will provide a superb education and experience, but they are different. None of them are obviously the “right” choice, most of us here are just offering our insight and advice about factors to consider.