When opening a magnet link from Chrome, Ubuntu will open its native torrent client Transmission, instead of Tixati. On first start, I enabled the torrent and magnet associations with tixati and I manually checked for associations with magnet links in the Shell Integration section of tixati's settings. Tixati claims its the default but it is not.

you have to make sure that chrome sees tixati as the default magnet link handler.

You mean in Settings > Advanced > Privacy > Content Settings > Manage Handlers? Because magnets links do not appear in that menu.

According to askubuntu chrome doesn't handle the magnet link, it just passes it straight through to the OS.

Instead, I had to run `gvfs-mime --set x-scheme-handler/magnet tixati.desktop` to set tixati as the handler. This post is a bug report about tixati being able to set these handler associations by itself. It incorrectly reports that it is indeed the default handler. I believe this is handled differently in Ubuntu 16.04, as Tixati could correctly configure handlers in 14.04.

same issue here

By same issue you mean that you are 1) on 16.04 LTS 2) using tixati as default handler under settings and 3) still cannot "import" magnet links into tixati??
Are you sure it is using correctly formatted links? GIGO abounds with .... sites. Have you ever used the Channels feature in tixati. You can join "Tixati User Group" for some support and they can definitely give you good magnet: links for verification of settings. :D