Automatic Duck Ximport AE can import media files with alpha channels into After Effects and set the alpha channel interpretation correctly, but it needs to know how to set the alpha interpretation and by default this information is not exported by Final Cut Pro X.
The solution is simple: edit a Metadata View in FCPX to include the Alpha Handling metadata property. Now use that Metadata View to export your XML from FCPX.
Want to learn more about Metadata Views? Philip Hodgetts wrote an excellent article for FCP.co all about the subject: The Power of Metadata Views in Final Cut Pro X by Philip Hodgetts