Nontrivial topological spin-textures, such as skyrmions, merons, bimerons, and skyrmioniums, are envisioned as robust building blocks for future memory and logic devices. Controllable transformations between these states require a quantum-mechanical description of electronic degrees of freedom and atomic-scale insight beyond existing phenomenological models. Here, we report an atomic-scale investigation of topological phase transitions and their protection in the two-dimensional van der Waals ferromagnet Fe$_3$GeTe$_2$ (FGT) using a combined experimental-theoretical approach. Synchrotron-based Fourier transform holography directly images labyrinth domains, isolated skyrmions, mixed labyrinth-skyrmion phases, and skyrmion bags with high spatial resolution. We compare these observations to simulations based on an electronic lattice Hamiltonian that captures both metallicity and relativistic spin-orbit coupling in FGT. By systematically exploring a broad range of temperatures and magnetic fields, we map the mechanisms governing topological transitions and their stability. This sequential-integrated experimental-theoretical framework advances understanding of spin-texture interactions and enables precise control of external tuning parameters. Our results establish a platform for creating, stabilizing, and manipulating topological states, paving the way for engineered spin-texture transitions in next-generation spintronic technologies.