There are only a few torrent clients that support I2P
- i2psnark
- qBittorrent
- BiglyBT
- XD
Also note that the only torrent client with DHT support via i2P is i2psnark, and only when using the standard java I2P. So in your case when using i2pd you can rule out torrenting via DHT. (BiglyBT sort of supports DHT but only when you manually click a button to force it to search DHT via I2P)
i2psnark standalone I think would still work for you (without DHT) but it is very, very feature limited when compared to standard torrent clients.
BiglyBT sort of works but it's not great as a full-time I2P torrent client, the devs purposely designed it to use I2P as a backup to regular clearnet torrenting. I'm not even sure if it's possible to configure it to be a full-time I2P torrent client.
That leaves you with qBittorrent and XD so those would be the ones you could check out. No idea about adding magnets or anything else via CLI but I do know there are tools that exist to do stuff like that for qBittorrent e.g. https://github.com/fedarovich/qbittorrent-cli
PS - Since you're not going to be torrenting with DHT it is important for you to make sure I2P trackers are added to every torrent you load otherwise you'll never find any torrent peers to connect to.
These are working public trackers in I2P that I know of:
http://w7tpbzncbcocrqtwwm3nezhnnsw4ozadvi2hmvzdhrqzfxfum7wa.b32.i2p/a
http://opentracker.skank.i2p/a
http://opentracker.r4sas.i2p/a
This tracker is also in I2P but it only tracks torrents registered at their site:
http://tracker2.postman.i2p/announce.php