>If my reading of the paper is correct, the unnatural XY base pair doesn't have any function per se, but without it the organism fails to replicate its DNA and quickly dies.

That's actually differently to how I've read it - it appears to me that the XY pairing is stable and not harmful to the host and so is not degraded or removed (recognised as foreign by mis-sense DNA proof readers) but is therwise not performing any function, although some of the technical details are missing.

As to your second point, we already have highly perfected 'terminator' technology, currently in 3 forms:

1) the infamous Monsanto terminator technology, where second generation seeds would not be viable (which, incidentally, would be a significant benefit to some farmers growing genetically engineered cotton and potentially their crops, as spilt seed from harvest would not germinate)

2) in bacteria and other organisms etc in the form that you describe above - ie lack of a substance is fatal - usually this substance is some generic low dose antibiotic that triggers a genetic switch when present

3) as you suggest, removing an organisms ability to synthesise a particular amino acid and having it dependent on food