I don’t think the tools have anything to do that, though it wouldn’t be too hard to add.
You can always do it yourself, go to Export(or bin)/flash/haxe and change either debug.hxml or release.hxml to replace swf with as3.
Not really the best solution if you want that each time though but in that case creating a new hxml and a shell script will work until you change a define or add a lib.