Now I am totally confused as well. I exported an unmodified master file (.cr2) from Aperture as well as one that had its exif data modified by HoudahGeo, the latter was showing the altered lens data when I exported it. Just to be sure I had done the export correctly, I reimported the two images into a new project. When I check the exif data on these two files the lens data is identical both showing the modified lens data. As an experiment I chose another image that shows lens data as "EF24-105mm f/4L IS USM" and chose Update From Master in Aperture and now the lens data is shown as "Canon EF 24-105mm f/4L IS".
Next test was to import a test image from the camera and lens into Aperture. Sure enough the exif data is shown as "Canon EF 24-105mm f/4L IS". So basically the problem is nothing to do with HoudahGeo or exifTool. It appears to be Aperture. I don't know if this is following an Aperture/OS X update but it seems to be a change within the last three months.
Thank's for the help with your side of things.