Yes, that's pretty much saying exactly what I said. God's omnipresence doesn't change, but he's given means ("means of grace") to make people more conscious/aware of his presence. Those means today often include (but are not limited to) churches.
Another example would be prayer at home. People talk about feeling "more present" with God when they pray, or that they "drew into God's presence" (there are various similar expressions that I'm sure you've heard). But these aren't affecting God's omnipresence in any way.
Like a lot of Philosoraptor "puzzles," it's just an apparent puzzle because he's equivocating terms and talking about two things that are actually different, but treating them as if they're on the same plane.