Programs meant to be ran by doube-clicking (rather than invoked as a command) generally are not meant to do anything until the user commands them to by clicking something else in their window. An application launching is meant to be kind of a "pure function", a side-effect-free operation (of popping up the app Window) from the user point of view.
If you design an app which writes anything into a document file as soon as you open the document in them you are doing it really wrong.
This given, the confusion you describe comes straight from lack of awareness of the UI metaphor logic in the software engineers. A well-designed GUI app (a non-GUI app should not be executed by double-clicking at all) would do virtually nothing to leave any traces (let alone break anything) right after you run them, by just launching them or "launching" any specific document to be opened in them.
But I get your point. From the practical point of view - given the reality, what we actually have, you are perfectly right.