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.
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.
Please don't remove downloads of .torrent files. If you don't have this it's impossible to know what files are in the torrent (or even how big they are!) without connecting to the swarm and relying on BEP 009 (Metadata exchange).
I use this all the time for downloading very long tail content, and the move to have indexing sites be magnet-only is very frustrating.
There is no intent, it's just there as many people still prefer torrent file. Though we have magnet links, so security focused users can download without us knowing nothing.