Halbeisen Combinatorial Set Theory on page 169 states "ZFA does not distinguish between the atoms and so a permutation of the set of atoms induces an automorphism of the universe".
How does the inability to determine the truth or falsity of "atom a = atom b = atom c = atom d" (assuming thats what the above means) affect the ability of ZFA to determine whether, for example,
{a} = {b}
or
{a,1}={b,1}
or
{a,b}={c,d}
To do this appears to require only the use of the $\in$ relation in the modified extensionality axiom (A is the set of atoms):
$\forall$x$\forall$y ((x $\notin$ A $\land$ y $\notin$ A) $\implies$ $\forall$z(z $\in$ x $\iff$ z $\in$ y) $\implies$ x=y)
The "Axiom of Atoms" suggests the $\in$ relation can be used on atoms, so can $\in$ not distinguish between atoms, e.g. to determine whether {a}={b}, is "a $\in$ {b}" not false?
ZFA is a formal system whose language is almost as spare as that of ZF. When you write down an expression with constants in it and ask if ZFA proves it, it's on you to explain how to actually define those constants in ZFA, and thus form a bona-fide sentence in ZFA's language. I suspect if you try that with some of the expressions you've written above, you won't have much luck, and, well, this is one way to understand what is meant by ZFA not distinguishing between the atoms.
Intuitively, within a model of ZF, we can take any set and unroll it into its transitive closure: make a with the set at its root, its elements at the next level, its elements' elements at the next level, and so on. Well-foundedness implies that after a finite number of levels, everything has terminated at sets with no elements. Extensionality implies each of these leaves are the empty set and working recursively back upwards we see that extensionality requires us to identify any two sets whose tree above is structurally identical. Any automorphism of the set will need to extend to an automorphism of this graph, since it was just built by the membership relation, so will need to map structurally identical subgraphs onto structurally identical subgraphs, and as we just said, these are necessarily the same set, so this action is trivial.
But when we allow atoms, no longer is every leaf necessarily the empty set, so the sets in the graph can no longer be distinguished only by the shape of the tree above: now we need to know which atoms are at the leaves as well. When we permute the atoms on the leaves, it results in a (possibly) distinct, but structurally identical set, so acts as an $\in$-automorphism of the set's transitive closure.
Note, there is morally nothing distinguishing the empty set from an atom (just as there is nothing morally distinguishing the various zeros in Asaf's analogy) , since they are just possible objects that go at the leaves (i.e. objects with no elements). The only thing that distinguishes is the fact that we have put the empty set into our language, so now any automorphism of a model must fix it by definition. You can think of the empty set as just an atom that's been distinguished as 'pure' by fiat, and the pure sets are the ones where all the leaves of their transitive closure is the empty set. We have not made any further distinctions amongst the atoms, and hopefully seeing how this aligns with the formalism closes the loop between my first paragraph and the long digression afterwards.