Does it mean that they exist in small amounts?
At all does indeed refer to small amounts, but only by way of comparison.
As per this answer, at all means "even a little bit", but the even is more important there than the little.
Sometimes, especially in casual contexts, people will use no or none to mean "not very much". Consider someone looking in a fridge and saying "there's no food" when there is in fact some things like a jar of mayonnaise and a bit of cheese, but not enough to make a meal out of. What they really meant was "there's so little food that there might as well be none".
To use at all underlines the difference between the casual none that could include "a little bit" and the precise none that cannot, but means absolutely none whatsoever. And likewise the difference between any that has some casual lower-limit and one that covers the slightest scrap, and so on:
"None at all": Not even the tiniest slightly amount.
"Any at all": At least a tiny amount (but possibly lots and lots).
"Not exist at all": There is absolutely none in existence whatsoever.
Okay. Let's consider the sentence with the parenthetical clause and the at all removed first:
Those heavy elements only exist because energy was put in to their manufacture in the dying explosion of a star…
There are some such elements because such explosions happened. Without such an explosion there would be none at all. Note that there's no statement about how much there actually is, just a binary of some vs. none.
Now we put the at all back in:
Those heavy elements only exist at all because energy was put in to their manufacture in the dying explosion of a star…
This means the same thing. The difference is that the fact that without such explosions there would be absolutely none at all is emphasised.
Now we put the parenthetical clause back in:
Those heavy elements only exist at all, and the energy is only available to be released, because energy was put in to their manufacture in the dying explosion of a star…
And we've extra information added about the fact that these elements can now partake in nuclear fusion. And we've arrived at the sentence you have.