@SHiLLySiT I don't believe so. It will still compile down to a single
.swf with the required bytecode to properly run.
The great thing about using the
.swc over the source is that you have a solid, constant baseline. If you make a game that works on the 2 July 2013 build of FlashPunk, you know you can always compile against it and get the same results; however, if you're building against a stack of files and you pull the latest changelist from GitHub, there's no telling exactly what will work or exactly what you need to do to go back to "version x" of your game.
If you like to hack on the source code, then you definitely should, but if you're setting out to make a game, you don't want your framework to change during development.