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I have a question about making bonding pads in magic. I want to create a passivation cut on the pad I am making, so I see sky130 has a "pad" layer. However, when I refer to a standard pad in the sky130 I/O library, the "glass" layer is used instead of the "pad" layer. What is the meaning of the "glass" layer - is it a glass cut/opening? Is there any documentation on this?

I believe the glass layer is the passivation cut. Haven't found any documentation on it before, so I'm also interested in this post

Yes, "glass" is passivation cut.  "pad" is equivalent to metal5 + a pad ID marker layer.

When I view my GDS in klayout after fill is added during tapeout, I see a "pad" layer instead of a "glass" layer. Whereas in magic I used the layer "glass" to create the passivation cut. Are these the same layers or is this something I should expect to see?

That's the same layer.  "PAD" is the official foundry name for the mask layer.  The layer name "glass" has traditionally been used in Magic for the passivation cut since the 1980s.