X-ray interferometry/holography was utilized to investigate the profile structures of n-hexadecyltrichlorosilane self-assembled monolayers (SAM’s), chemisorbed onto the SiOx surface layer of Ge/Si multilayer substrates fabricated by molecular beam epitaxy, in their initial "as deposited" form and throughout an annealing process. This approach permitted an unambiguous determination of the electron density profiles of the various layers within the inorganic multilayer substrate and the chemisorbed SAM overlayer, including the smoothness/roughness of the interfaces between adjacent layers, to relatively high spatial resolution without any prior assumptions. The corresponding in-plane structures of these various forms of the SAM’s were investigated by high Delta Q-resolution X-ray diffraction. The interpretation of the latter results was greatly facilitated by comparison with analogous kinematical structure factors calculated from molecular dynamics computer simulations of an ensemble of alkyl chain molecules "chemisorbed" onto a planar surface as a function of in-plane molecular density and temperature. Our results indicate that the initial "as deposited" and "high-temperature" forms of these SAM’s consist of small domains of highly tilted chains (relative to the normal to the monolayer plane) within a positionally-disordered distorted hexagonal in-plane lattice, consistent with the dominance of chain-chain interactions. Upon cooling and drying, substantial structural reorganization takes place within the SAM and the SiOx substrate surface layer resulting in the predominant "annealed" form of these SAM’s consisting of larger domains of much less tilted chains within a positionally-disordered hexagonal in-plane lattice, consistent with the dominance of chain headgroup-surface interactions. While such annealing produces only a modest increase in the in-plane interchain correlation length, the so-"annealed" SAM’s are then structurally stable over the 293-363 K temperature range investigated, consistent with their intradomain structure.