The idea of employing non-Abelian statistics for error-free quantum computing ignited interest in recent reports of topological surface superconductivity and Majorana zero modes (MZMs) in FeTe$_{0.55}$Se$_{0.45}$. An associated puzzle is that the topological features and superconducting properties are not observed uniformly across the sample surface. Understanding and practical control of these electronic inhomogeneities present a prominent challenge for potential applications. Here, we combine neutron scattering, scanning angle-resolved photoemission spectroscopy (ARPES), and microprobe composition and resistivity measurements to characterize the electronic state of Fe$_{1+y}$Te$_{1-x}$Se$_{x}$. We establish a phase diagram in which the superconductivity is observed only at sufficiently low Fe concentration, in association with distinct antiferromagnetic correlations, while the coexisting topological surface state occurs only at sufficiently high Te concentration. We find that FeTe$_{0.55}$Se$_{0.45}$ is located very close to both phase boundaries, which explains the inhomogeneity of superconducting and topological states. Our results demonstrate the compositional control required for use of topological MZMs in practical applications.
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