Boagie, you are referring, then to existence as a whole, not nature in particular, which has many instances of caring.
I think that this is more a question of how we use adjectives than one of metaphysics. (though I contend that nearly all metaphysical "problems" boil down to linguistic matters in the end)
For instance, do we even expect NATURE to care? If not, what use is it to describe it as indifferent? It's like commenting that domesticated cattle in North America are flightless and illiterate. Well, since no one really expects to see a cow that can fly or read, the characterization is sort of superfluous.
Another problem is whether we can speak in generalities like this when it's a matter of "vector addition". Most things in nature don't care, but some things do. Since the sum of the vectors points to indifference, does that mean we can call it one of nature's most enduring qualities as If it's just one quality applied to just one thing?
Most animals on earth lay eggs -- nearly all invertebrates, most vertebrates, and all but a few mammals. So does that mean that oviparity is one of the fundamental qualities of animals? No, it's simply a very common one.
Yes, it's semantics, but I'm not the first to contend that all metaphysical problems are nothing more than semantic vagaries and fault lines.
Indifference is a meaning, the physical world is deviod of all meaning, only through a subjects experience of the physcial world and his feelings about that physical world in relation to his own biology is meaning formed in a conscious subject, which is then bestowed upon the world. In a very real sense, each subject is the centre of the universe. So, indifference is the emotional experience of a subject. I hope that covers it, but if not, alert me to what I have missed.
The problem you posed in the introductory post is one that looks completely different depending on subtleties of semantics. The indifference of nature and the indifference of existence could have been used interchangeably to make the exact same point in your first post -- and yet the former poses very different conundra and exceptions. So there's no getting around the semantics unless we can all agree on exactly what you meant. I'm not willing to apply an adjective to all of "nature" when there are many "natural" exceptions. Nature isn't one thing -- it's an infinitude of instances, and I think it can only be spoken of as one thing in a colloquial way.
Whether or not that indifference we experience is an issue would depend on the expectations of the subject. To what extent that perceptional aspect, in which we imbue nature with this behavioral word 'indifference', makes our world 'cold', depends on the perceiver.
There's a number of ways we can look at this. I blogged this a while back (not exactly along these lines, but close) at this link.