So we've got the nucleus - we know the mass of that.
We know the mass of a free unbound electron.
We know the energy an electron gives of as it becomes bound.
In the classical particle electron would it have relativistic mass at its lowest energy level?
If there is relativistic mass this is being weighed when measuring an atom's mass.
Refer back to "The Concept of Mass" previously linked.., there is no "relativistic mass" there is just mass. Sometimes referred to as invariant mass, inertial mass, gravitational mass or rest mass. They are all the same thing and relativistic mass is a confusing and misleading description for the TOTAL energy, of an invariant mass plus any kinetic energy associated with its velocity.
While E is generally used to denote total energy, the total energy it refers to is defined by the context it is used. In the equation E = mc^2, it referrs only to the total energy associated with a specific invariant mass. It does not include any energy associated with acceleration or velocity.