It is commonly assumed that topological phase transitions in topological superconductors are accompanied by a closing of the topological gap or a change of the symmetry of the system. We demonstrate that an unconventional topological phase transition with neither gap closing nor a change of symmetry is possible. We consider a nanoscopic length ladder of atoms on a superconducting substrate, comprising self-organized magnetic moments coupled to itinerant electrons. For a range of conditions, the ground state of such a system prefers helical magnetic textures, self-sustaining topologically nontrivial phase. Abrupt changes in the magnetic order as a function of induced superconducting pairing or chemical potential can cause topological phase transitions without closing the topological gap. Furthermore, the ground state prefers either parallel or anti-parallel configurations along the rungs, and the anti-parallel configuration causes an emergent time reversal asymmetry protecting Kramers pairs of Majorana zero modes, but in a BDI topological superconductor. We determine the topological invariant and inspect the boundary Majorana zero modes.