Yes, it is true that PI now uses APIC-EM for PnP. In terms of differences, think of APIC-EM as a programmatic layer on top of the network (meaning you can extract things like topology, inventory, and network state programmatically). Today, it does PnP, IWAN provisioning, and flow-based path trace. All of these are also driven by a REST-based programmatic interface. Think of PI as a network management application in that it does element, config, and fault management. What you'll see is that more and more network services will be exposed from APIC-EM that PI can take advantage of, so that PI becomes a set of applications on top of APIC-EM.
I want to add that while you can use APIC-EM without PI to do PnP today, PI adds a layer of value on top of APIC-EM in that it manages the config templates and software images, and uses the APIC-EM REST interface to drive the provisioning of new devices. Without PI, you'd likely have to build your own application to do this management.
In terms of investment, APIC-EM is freely available. The IWAN feature, however, is cross-licensed with PI, so if you've invested in PI, then you have a license for the APIC-EM features as well.
