Magnet links are perfectly fine for popular content, but because of the dependency on BEP 009 (Metadata exchange) for very long tail content it's often better to get the torrent file directly.

For example, to get information about torrents that are on life support (e.g. have a couple seeds that show up for a few minutes a day), having the torrent file downloadable is invaluable, as it includes info like the size and the file names, etc. In many cases it's even possible to bring a torrent /back to life/ if you have the torrent file and got the content that was in it out of band.

If you just have the magnet link you cannot do any of this.

It's not the same.you'll be missing some of the trackers.

Magnet URLs can and usually do include all of the trackers.

http://www.bittorrent.org/beps/bep_0009.html#magnet-uri-form...

That being said DHT and PEX (BEP 5 and BEP 11) is good enough that you don't need them.

That's not entirely true. DHT is generally the most effective, but PEX and trackers help a lot when there aren't many seeds, or there's a lot of noise on the DHT.