Unfortunately, comparing configurations within the IAR IDE requires lots of switching back and forth between configurations and the multitude of configuration categories and tabs.
A better way exists to compare configurations, albeit with a few manual steps:
IAR keeps the configurations in an xml file with .ewp extension, SimpleBLEPeripheral.ewp for example. Each configuration is contained in a block marked by <configuration> and </configuration>
Using a text editor, extract the configurations that interest you, each into a separate text file, then simply diff the text files (e.g. winmerge).
For example, comparing "CC2540F128DK-MINI Keyfob" to "CC2540" shows the main difference to be:
< <state>HAL_LCD=FALSE</state>
< <state>HAL_LED=TRUE</state>
< <state>CC2540_MINIDK</state>
---
> <state>HAL_LCD=TRUE</state>
> <state>HAL_LED=FALSE</state>