I think you have a great misunderstanding of that lore paragraph, as I see it anyways. One section in particular states,
"However, being broken down to the aetheric level can take its toll on one's body, and rest is often required after several consecutive jumps, especially as the distance becomes greater."
Notice the bold section. As I understand this, any negative effects that result from teleporting are threshold effects. What this means is that nothing bad happens until a certain number of jumps, within a certain span of time, are made. Interpreting this with anima would mean that 100 anima is that threshold. If you could jump into the negatives then, maybe, you would start showing signs of over teleportation. Up until this point you should be fine. It might also be worth mentioning that death and teleporting aren't necessarily related, as the physical effects on the body may be different for each event. It's really hard to say in a fantasy world.
Really though, lore aside, there's absolutely no need to place such a penalty on players. It's overly harsh and makes the entire gaming experience far more stressful. Any kind of death penalty should, in my mind, only result in lost time and perhaps money, within reasonable bounds. Losing xp in XI was losing time. Gear repairs in XIV is losing gil. Teleporting back to your home point, in both games, is losing time. Placing status effects, forcing NM engagement, or restricting what people are able to do by removing their ability to travel are far beyond any reasonable punishment for death.
After reading many of your suggestions and posts though, I am thoroughly convinced you don't actually care about what's good or fun, and only seek to damage systems you don't personally like. We shouldn't be focused on making things harder or more annoying, we should be focusing on ways of making the game enjoyable for everyone.
Edit: Just thinking about it for a moment, I realize you might try to say that removing anima is just adding to the time necessary to get places, which is true. I don't have a fantastic reasoning against that, to be honest. My best attempt though would be to say that it's a matter of intensity. If I recall correctly, at high levels in XI you'd only lose 10% experience of your level, rather than 50% or 100%. Same here, you lose time by being taken to your homepoint, but aren't also punished with slower movement. It's all about finding a proper balance and as it is now, I'd say it's balanced. Sorry, this post was way longer than I expected lol.