Keep in mind there is a cap on magic resistance which I believe also applies to absorb. You cannot reach 100%.
Magic resistance has a cap. Spell absorption does not. I most certainly can become totally immune to spells (and diseases, etc.) for 60 seconds once a day.
It is weird until you look at the guts of the game. If it is not physical damage from a weapon strike, then it is some kind of spell effect that does the damage. Poison and Disease are really Spell Effects at their core. Does not mean it is working quite right, but that is why it is what it is.
Yes, I'm very familiar with the game mechanics of the Oblivion and Fallout 3 engines this game was built on. I understand how a lot of this stuff is implemented. But like you've said, some of these things are very much not spells. Diseases and giants slamming the ground should not be getting absorbed, but they are. Disease, for example, is being treated like it's an enchantment. It shouldn't be getting treated that way.
I suppose that would include shouts and dragon breath...
No, the Thu'um is actually magic. It's correct for spell absorption to eat that, and it does. Noticeably, I don't seem to receive magicka for absorbing shouts/breath, which makes sense because they don't cost magicka. That's why I found it so odd that I'm getting magicka from things like disease. If I had to guess (and without the Creation Kit, I do), I'd think disease chance actually
is an enchantment placed on the creature weapon. The enchantment is likely set to be free, but its base cost is what I'm absorbing still.