No, CS4 does not treat this any differently than previous versions. Export to Flash (XFL), the new "roundtripping feature", only works from AE (or InDesign) to Flash, but not the other way around. Beyond that I'm not clear what you are asking - SWFs are treated as continuously rasterized vector art, including any transparencies. If you export them accordingly from Flash, they should come in just fine in AE.

Mylenium