Topological insulator nanowires with uniform cross section, combined with a magnetic flux, can host both a perfectly transmitted mode and Majorana zero modes. Here we consider nanowires with rippled surfaces---specifically, wires with a circular cross section with a radius varying along its axis---and calculate their transport properties. At zero doping, chiral symmetry places the clean wires (no impurities) in the AIII symmetry class, which results in a $mathbb{Z}$ topological classification. A magnetic flux threading the wire tunes between the topologically distinct insulating phases, with perfect transmission obtained at the phase transition. We derive an analytical expression for the exact flux value at the transition. Both doping and disorder breaks the chiral symmetry and the perfect transmission. At finite doping, the interplay of surface ripples and disorder with the magnetic flux modifies quantum interference such that the amplitude of Aharonov-Bohm oscillations reduces with increasing flux, in contrast to wires with uniform surfaces where it is flux-independent.
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