I know this looks really weird, here is why:
The first time the makefile is run, in the project root, the first part of the if is triggered.
This part of the makefile records the root directory and creates the bin diretory.
Then it runs itself in the bin diretory. This triggers the else part of the makefile.
The last bit of magic is that VPATH=... line.
The VPATH is a special make variable that specifies extra directories to search for dependencies in.
This particular assignment of VPATH allows make to find sources from the root, but forces all results to be in the bin dir.

This has two benifits:
1. the makefile is written as if it's in the project root, but results are always in bin
2. the clean phony target may just remove bin, as this is always correct

The prior implementation of the efm32 makefile templates used a custom version of the bin diretory creation.
My version has a few advantages:
1. the targets are always forced into bin.
   this is different from the old style, where any custom rules might polute the project root directory
2. smaller templates
3. fewer total templates