How is it best to avoid issues like these without having to get approval by a 3rd party? Is coding it at home and sending it to one's office email address enough for documentation that it was done in non-office time?
It's not even a matter of developing it on non-office hours using non-office equipment. Clauses are usually more broad to stop someone from creating a competing product, even when not on company time. Having built an app designed specifically for company systems, the company would likely have a legal claim against the invention, even if it were developed outside of office hours.
I can see that problem for a situation where the outcome turns into a marketable product. But in these automatization cases it looks more to me like when somebody running a horse-drawn carriages business starts suing an employee for working in his free time on developing a car. The skills by the employee applied to solve the problem seem often unrelated/overqualified for the reason they were hired.