We investigate the Kitaev-J₃ honeycomb model using variational Monte Carlo calculations combined with a vison-quasiparticle analysis of the parent Kitaev spin liquid (KSL). We provide evidence for deconfined magnetic phases in which zigzag or antiferromagnetic order coexists with remnant Z₂ topological structure inherited from the KSL. The optimized variational wave functions retain multiple linearly independent topological sectors on a torus, whereas those of conventional ordered phases collapse to a single sector. The vison-quasiparticle analysis shows that magnetic order naturally arises from vison-pair condensation while single visons remain gapped, yielding a microscopic mechanism for magnetic ordering without immediate confinement. The resulting phases further host gapless spinons with multiple Majorana cones, offering a possible microscopic scenario for the anomalous low-temperature longitudinal thermal transport reported in magnetically ordered Kitaev materials such as Na₂Co₂TeO₆. Our results reveal a microscopic route to fractionalized magnetism beyond the conventional dichotomy between magnetic order and spin-liquid behavior.