Scope is the response of Lagrangian flow topologies of three-dimensional time-periodic flows consisting of spheroidal invariant surfaces to perturbation. Such invariant surfaces generically accommodate nonintegrable Hamiltonian dynamics and, in consequence, intrasurface topologies composed of islands and chaotic seas. Computational studies predict a response to arbitrary perturbation that is dramatically different from the classical case of toroidal invariant surfaces: said islands and chaotic seas evolve into tubes and shells, respectively, that merge into “tube-and-shell” structures consisting of two shells connected via (a) tube(s) by a mechanism termed “resonance-induced merger” (RIM). This paper provides conclusive experimental proof of RIM and advances the corresponding structures as the physical topology of realistic flows with spheroidal invariant surfaces; the underlying unperturbed state is a singular limit that exists only for ideal conditions and cannot be achieved in a physical experiment. This paper furthermore expands existing theory on certain instances of RIM to a comprehensive theory (supported by experiments) that explains all observed instances of this phenomenon. This theory reveals that RIM ensues from perturbed periodic lines via three possible scenarios: truncation of tubes by (i) manifolds of isolated periodic points emerging near elliptic lines or by either (ii) local or (iii) global segmentation of periodic lines into elliptic and hyperbolic parts. The RIM scenario for local segmentation includes a perturbation-induced change from elliptic to hyperbolic dynamics near degenerate points on entirely elliptic lines (denoted “virtual local segmentation”). This theory furthermore demonstrates that RIM indeed accomplishes tube-shell merger by exposing the existence of invariant surfaces that smoothly extend from the tubes into the chaotic shells. These phenomena set the response to perturbation—and physical topology—of flows with spheroidal invariant surfaces fundamentally apart from flows with toroidal invariant surfaces. Its entirely kinematic nature and reliance solely on continuity and solenoidality of the velocity field render the comprehensive theory and its findings universal and generically applicable for (arbitrary perturbation of) basically any incompressible flow—in fact any smooth solenoidal vector field—accommodating spheroidal invariant surfaces.