Isotopes are only imperfect in the context of one labeling system. But not from a quantum viewpoint.
Once something that you thought was atomic actually shows variation you begin to suspect it is composed of smaller things.
Your comment does remind me of this though: https://en.wikipedia.org/wiki/One-electron_universe
If we are not in a one-electron universe, every electron is unique in the sense that it has an entirely unique path though spacetime, and thus can't be identical. I think what you mean is that every one of these "particles" seems to obey the same set of laws, which is not something that's unique to atoms, subatomic particles, or even larger things like molecules.
No, quite the opposite, actually. Some particles being identical is core to many quantum mechanical ideas. The distinction between Bosons and Fermions fundamentally relies on this idea.
Also, it probably isn’t true that all electrons have individual well-defined paths through spacetime.
Electrons are Fermions.
When two electrons are “in orbit” around a helium nucleus, with the atom including the electrons being in the lowest energy state, the two electrons are orbitals distinguished by their spin, but, at least if it were not for the interaction with the magnetic interaction from the spin of the nucleus, you could choose any axis along which to consider the spin direction of the electrons, and like, you would get for each of the two spin directions along that axis, one of the electrons would have its spin in that direction. But considering different axiis for the spin, you would be splitting the two up in different ways?
I’m fairly confident it isn’t possible to assign a consistent id for each electron which persists through time. (Even setting aside the “they don’t have well-defined positions” aspect)