When you create a Flex library project, the default configuration is to mark framework linkage as external.
This make sense if you add the library project on another project, since this project will include the framework classes the library will use.
Three reasons to mark framework linkage as merged into code are
1/ framework-independant SWC, to avoid future changes in framework which could break code
2/ code loaded as module
3/ AIR Native Extension
On previous versions of Flash Builder, you had to link on ANE's SWC and to make the magic works, you had to use external link type.
So, I assume it's still doing the same behind the scene on Flash Builder 4.6+
If it uses external linking, the SWC will work as a standalone library so you need to include any (sub)classes used ...hence the framework classes used must be included.