With torrents, you see the files in the torrent so you can select which to download before starting the download of the torrent content.
With Magnet links that's no possible. You have to wait until the Magnet link has been downloaded, then manually pause, select files and restart the download.
At that point, Transmission may already have started creating .part files for some files that you don't want.
Waiting for the Magnet link to be downloaded can sometimes take several minutes.
Feature requests for the Mac OS X version of Transmission
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