Charge transport in electronic applications involving molecular semiconductor materials strongly depends on the electronic properties of molecular-scale layers interfacing with external electrodes. In particular, local variations in molecular environments can have a significant impact on the interfacial electronic properties. In this study, we use scanning tunneling microscopy and spectroscopy to investigate the self-assembly regimes and resulting electronic structures of alkyl-substituted quaterthiophenes adsorbed on the Au(111) surface. We find that at dilute molecular concentrations, dimerized cis conformers were formed, while at higher concentrations corresponding to small fractions of a submonolayer, the molecular conformation converted to trans, with the molecules self-assembled into ordered islands. At approximately half-monolayer concentrations, the structure of the self-assembled islands transformed again showing a different type of the trans conformation and qualitatively different registry with the Au(111) lattice structure. Molecular distributions are observed to vary significantly due to variations in local molecular environments, as well as due to variations in the Au(111) surface reactivity. While the observed conformational diversity suggests the existence of local variations in the molecular electronic structure, significant electronic differences are found even with molecules of identical apparent adsorption configurations. Our results show that a significant degree of electronic disorder may be expected even in a relatively simple system composed of conformationally flexible molecules adsorbed on a metal surface, even in structurally well-defined self-assembled molecular layers.