Interesting, if a bit long perhaps. Also, I've never heard I/O instructions being referred to as "infrastructure instructions" before, can this be a mistranslation?
I/O is anything outside the program itself. All sorts of headaches happen this way. The problem is actually more complex than the article suggests. For example, say your app uses a database schema. What if the schema changes? Will your app break?
The reason the name "infrastructure instruction" was coined for this article is that it includes instructions such as "int", "rdtsc", which do not deal with only input and output, but deal with more complex things inside a CPU, such as timers and CPU privilege levels.