In several places I've worked, the business users and IT departments have made the decision to customize commercial software, imparting their own special flavors of it instead of accepting the base functionality. IT people like to solve problems, but I think modifying off-the-shelf software is usually bad practice. It leads to more complex upgrades and a failure to examine business practice. We should more often ask: "are we really unique? Why couldn't we use the software as it is? It's been proven for other businesses."
Certainly, if we run the same software as our competitors, we lose competitive advantage. We should customize only where it makes sense, not in proven functionality like G/L and payroll.