Racemic perhydrotriphenylene (PHTP) forms a polar inclusion compound with 1-(4-nitrophenyl)piperazine (NPP) as a guest molecule. Homochiral stacks of PHTP molecules surround polar chains of hydrogen-bonded NPP molecules in a channel-type, honeycomb architecture. The NPP chains are arranged in an all-parallel (rather than an antiparallel) fashion. Crystals of [PHTP](5)[NPP] show second harmonic generation for incident light of wavelength 1064 nm, an electro-optical and a pyroelectric effect. The X-ray diffraction pattern exhibits Bragg-like reflections, interspersed with planes of diffuse scattering and weak satellite reflections superimposed on these planes, features which are indicative of extensive disorder. In spite of this, an orthorhombic average structure model could be deduced from the Bragg-like reflections (space group Cmc2(1), a = 15.023(2), b = 23.198(2), and c = 4.730(1) Angstrom (T = 100 K), wR(2) = 0.088, goodness of fit 1.38). A qualitative interpretation of diffuse and satelite scattering is given. Crystals of [PHTP](5)[NPP] are approximately hexagonal prisms. If the tailor-made additive 1-(p-tolyl)piperazine (TP) is present during crystallization, the habit changes to approximately hexagonal plates and TP is incorporated in small amounts. Crystals of the composition [PHTP](5)[NPP](0.93)[TP](0.07) lose the ability of second harmonic generation. The observation of polar properties for a crystal structure whose polar building blocks, the -NO2...HN-hydrogen-bonded NPP chains, are 14-15 Angstrom apart and separated by PHTP hydrocarbon molecules is surprising, but can be explained in terms of a Markov chain model of crystal growth. The same simple model accounts for the loss of polarity in the presence of the tailor-made additive TP. The knowledge gained during the present analysis provides a rational tool for the engineering of polar properties of PHTP and similar channel-type inclusion compounds.