Thermal radiative phenomena can be strongly influenced by the coupling of phonons and long-range electromagnetic fields at infrared frequencies. Typically employed macroscopic descriptions of thermal fluctuations often ignore atomistic effects that become relevant at nanometric scales, whereas purely microscopic treatments ignore long-range, geometry-dependent electromagnetic effects. We describe a mesoscopic framework for modeling thermal fluctuation phenomena among molecules near macroscopic bodies, conjoining atomistic treatments of electronic and vibrational fluctuations obtained from density functional theory in the former with continuum descriptions of electromagnetic scattering in the latter. The interplay of these effects becomes particularly important at mesoscopic scales, where phonon polaritons can be strongly influenced by the objects' finite sizes, shapes, and nonlocal or many-body response to electromagnetic fluctuations. We show that, even in small but especially in elongated low-dimensional molecules, such effects can modify thermal emission and heat transfer by orders of magnitude and produce qualitatively different behavior compared to predictions based on local, dipolar, or pairwise approximations.