After a SWF is published, will it work OK if the SWF is then converted to a Flash Projector to run off a CDROM rather than as an installed Air application? The clients we work with (and their clients as well) will all balk at having to go through an install process with the Air application. Their IT departments will really be against it.
A Catalyst SWF is a perfectly normal Flash 10 SWF, so turning it into a projector should be fine. Make sure you use the run-local version of the SWF.