The issue boils down to: how stand-alone is the application? If it's totally stand-alone, then the data implementation can be solely for the convenience of the app designer (or user if it's in Excel). But those apps are few and far between: most companies want to see reports, gauge effectiveness, share a customer master and a product master and to measure ROI. Stand-alone apps are rarely designed for that "enterprise vantage."
If the data is a shared resource, then it's an enterprise resource and needs to be managed and designed as such.
It's like the difference between a go-kart and a Hummer. The go-kart is lots easier to build, and may have some specialized military usage. But the Hummer is the better choice for most battles.