The compiler is not able to do incremental compilation (at least not when used by Flex Builder 3.0 Alpha for Linux). So it compiles all project sources on every build, including all included classes. The only exception is classes that are included from SWC libraries: SWC libraries are not re-compiled on every build. So if you compile all external referenced third-party classes into SWC libraries, and also perhaps the already finished components of your own project, you can greatly increase build speed. Just remember, if file size of the final SWF file matters to you, do the last build before real-world deployment with including classes from ActionScript source files instead of libraries, as including a whole library will include many unused classes.
When using these instructions, Flex Builder for Linux 3.0 Alpha might temporarily not be able to present code suggestions (like code completion on Ctrl+space) to you from the code that you now include as a library. But it is able to do so without regard to how you add third-party code to use in completion (library or source path). To correct this issue, in the project properties in “ActionScript Build Path: Library Path”, delete the library entry and add it again (as a ActionScript Library Project or SWC, last position is fine).