This paper aims to reconstruct the internal structure of a two-dimensional test object via numerically simulated full-wave time domain radar tomography with the presence of carrier wave induced (carrier-induced) uncertainty, following from a complex domain structure, and short wavelength of the signal as compared to the target object diameter. In particular, we consider an application in planetary scientific studies of reconstructing the interior structure of an arbitrary high contrast small Solar System Body (SSSB), i.e., an asteroid, with a probing signal of small wavelength following from the instrument and mission payload limitations. Our uncertainty reduction model is devised from the statistical viewpoint by finding the reconstruction via multiple datasets assuming that the carrier-induced deviations in the reconstruction correspond to random deviations, which are independent and identically distributed (IID) for each dataset. A spatial and frequency-based error marginalisation is implemented, thus inspecting the relationship between the signal baseband frequency and the phase discrepancy of the modelling accuracy, determined by the signal and domain parameters. The numerical experiments are performed for 20 and 60 MHz center frequencies proposed for CubeSat-based radars. Of these, the latter matches the center frequency of the Juventas Radar which will be aboard HERA mission to investigate the interior structure of asteroid Dimorphos, the asteroid moon of the binary system 65803 Didymos.