Those examples are different because they are core to each of those companies' business model by being directly tied into their revenue stream. Simply put, it makes them competitive. Therefore, those apps you mentioned have to be good if not better than what their competitor uses.
The problem is more about internal applications that have nothing to do with the identity of the company itself. Personnel management, time tracking, accounting, and payroll apps suffer from poor quality if built in-house because they are part of the cost of doing business independent of what that business may be.
And that's the irony of it. Why do companies think they are going to innovate in the area of personnel management, time tracking, accounting and payroll in such a way that it'll give them an advantage over their competitors who also need to do this? These are commodity processes, or should be, and should be deployed from proven, mature technologies. The fact that they are commodities means they should be cheap. The fact that this isn't the case means this industry is broken (again most likely because the people tasked with deploying these processes/services are not going to be the ones using them).
The problem is more about internal applications that have nothing to do with the identity of the company itself. Personnel management, time tracking, accounting, and payroll apps suffer from poor quality if built in-house because they are part of the cost of doing business independent of what that business may be.