We extend the anholonomic frame and connection deformation method, AFCDM, for constructing exact and parametric solutions in general relativity, GR, to geometric flow models and modified gravity theories, MGTs, with nontrivial torsion and nonmetricity fields. Following abstract geometric or variational methods, we can derive corresponding systems of nonmetric gravitational and matter field equations which consist of very sophisticate systems of coupled nonlinear PDEs. Using nonholonomic frames with dyadic spacetime splitting and applying the AFCDM, we prove that such systems of PDEs can be decoupled and integrated in general forms for generic off-diagonal metric structures and generalized affine connections. We generate new classes of quasi-stationary solutions (which do not depend on time like coordinates) and study the physical properties of some physically important examples. Such exact or parametric solutions are determined by nonmetric solitonic distributions and/or ellipsoidal deformations of wormhole hole configurations. It is not possible to describe the thermodynamic properties of such solutions in the framework of the Bekenstein–Hawking paradigm because such metrics do not involve, in general, certain horizons, duality, or holographic configurations. Nevertheless, we can always elaborate on associated Grigori Perelman thermodynamic models elaborated for nonmetric geometric flows. In explicit form, applying the AFCDM, we construct and study the physical implications of new classes of traversable wormhole solutions describing solitonic deformation and dissipation of non-Riemannian geometric objects. Such models with nontrivial gravitational off-diagonal vacuum are important for elaborating models of dark energy and dark matter involving wormhole configurations and solitonic-type structure formation.