There is a difference between these variables. CMAKE_SOURCE_DIR does indeed refer to the folder where the top-level CMakeLists.txt is defined. However, PROJECT_SOURCE_DIR refers to the folder of the CMakeLists.txt containing the most recent project() command.
For example, say you have a top-level project called Outer and this contains a subdirectory with its own project called Inner. Outer‘s CMakeLists.txt has:
project(Outer)
add_subdirectory(Inner)
and Inner‘s:
project(Inner)
Then in both of these CMakeLists files, CMAKE_SOURCE_DIR will refer to Outer‘s source dir. But while PROJECT_SOURCE_DIR for Outer is also this same dir, this is not the case for Inner. Inner‘s PROJECT_SOURCE_DIR is the subdirectory containing its CMakeLists.txt.
This difference applies to all PROJECT_<var> vs CMAKE_<var> variables.