If you're like most companies using SAP HR, by now you've invested millions of $ in licensing, support, maintenance and enhancements. SAP HR now provides functionality for pretty much every HR function, from recruitment to payroll, though most companies haven't implemented all of it. You've established a support organization that knows how to configure SAP HR and accomplish most of your ABAP and Portal development.
So let's assume you want to implement something new now - Recruitment, Compensation Management, Workforce Analytics, etc. The HR organization likes the user interface and breadth of functionality in some 'best of breed' software package that is not SAP. The equivalent SAP functionality meets 80% or 90% of HR's requirements and it doesn't have as good of a user interface. Which way do you go? License new software, build interfaces and integration from it to SAP HR, install new infrastructure (hardware, training support staff, etc); or use the SAP HR software you already have, spend some development effort to bridge that 10% to 20% functionality gap, and do some things to make it look pretty? How formal do you get in your cost/benefit or ROI analysis?
Some companies have a policy that if the functionality is in SAP HR, they use it. If the functionality doesn't quite meet their needs, they develop enhancements or bolt-ons to fill the need - but it is clear that you better have a really good reason not to use SAP HR. At the other end of the spectrum, SAP HR is simply one piece of software to achieve some functional needs - it does the HR administration, for example, and other software modules are used as needed for specific purposes. The HRIS landscape is a collection of best-of-breed systems that are interfaced and integrated to achieve the HRIS function.
So which way is the best one? They can both work fine! Though my preference is to use as much of the SAP HR software as possible, either method can work if done correctly, with planning, purpose, and discipline. If either approach is done haphazardly, well, you get some haphazard results. The important thing is to do it well - the nuts and bolts of determining business needs, defining requirements, implementing them in the software, and change management both for process-users and the HR/IT staff.