As I understand it (I'm not on a Mac) When you open a new presentation the slide added has the first custom layout (usually but not always a Title Slide Layout). Unless you use the drop menu the next slide has the second layout. Future slides have the last used layout UNLESS it was the first layout in which case the second layout is used.
Not sure what you mean "isn't the master slide supposed to insert". The master slide never inserts it is always based on a layout.
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