1.) The command used to build a Flex application (via IDE option) contains "-library-path xxx". So, if I configure a whole directory with SWCs (in project dependencies), this excludes all Flex framework SWCs which must then be added manually. The preferred option would be "-library-path+=xxx" - this keeps all Flex SDK libraries configured in "flex-config.xml" and adds the ones configured in IDEA.
2.) Single SWCs added to the project are handled via "-include-libraries xxx". This leads to inclusion of all classes in the SWC, regardless if they are used or not. I would prefer SWCs added via "-library-path+=xxx.swc" (like above, the MXML compiler is smart enough to differentiate between explicit SWCs and directories with SWCs).