Much like any receiver's built-in amps compare to standalone amps, I'd suspect. Smaller power supply, less total power, less capable at managing difficult loads (low-impedance speakers in particular, but also low-efficiency speakers), and not as capable of naturally-ventilated cooling due to space limitations.

Here's the simple "visual aid" analogy: look at the space available in the left and right sides of the Model 990's cabinet (which is where the seven amp channels of the R-965 were housed - we can anticipate similar or even more severe space limitations on the R-972 since it's in the same chassis). This picture (from the Pictures page in my sig) will help. The R-965's internal amps were rated at 120W/channel. Now look at the Model 7125, which is rated at just 5W more per channel. Again, this picture (taken from the same page) gives some idea of what the 7125 looks like inside. The larger power supply, the heat sinks, and the additional room for each channel are easy-to-identify reasons why the 7125 will be capable of doing more than a "wattage equal" receiver.