This is really confusing to me, as a registered European and UK patent attorney.
The FFG jacking out article calls it a “mechanics license”. The relevant intellectual property right for card game mechanics is patents. You can patent game mechanics, but it isn’t done very often (you can find some Andrew Looney US patents to game components and mechanics if you go look for them). Unless they’ve registered it under an unusual name, I cannot find a WotC patent to anything related to Netrunner. So that’s out.
So, trademarks. There were several registered US trademarks to “Netrunner” assigned to WotC, but they’ve been expired for years. I’m not a US attorney so I’m not going to pretend to know anything about the laws of unregistered marks, but it seems odd to not have a registered right if there’s a license agreement around the use of that right.
Which leaves copyright. Copyright would cover literal card text, but not the mechanics covered by that text. I don’t know the US case law around copyright in single words, but it would be extremely shaky in the EU.
So my best guess about the agreement is that it was a bespoke contract rather than any license of IP rights, because I don’t think there’s much relevant IP, in the legal sense, at issue here (with clauses about who owns the copyright in the card text and art, as Netrunner cards have WotC and FFG copyright notices on them). I have absolutely no idea how enforceable a contract that says “you’re not allowed to use these game mechanics that we don’t actually have IP protection for in any way shape or form after this expires” because I’m not a US contract lawyer but… it sounds pretty flimsy to me.
If you’re thinking “well I’m sure FFG would know their rights here”: I have worked with much, much bigger companies than FFG who have had absolutely no clue about this side of things, so it’s certainly not an assumption that I’m making.