The production of the $X(3872)$ particle in heavy-ion collisions has been contemplated as an alternative probe of its internal structure. To investigate this conjecture, we perform transport calculations of the $X(3872)$ through the fireball formed in nuclear collisions at the LHC. Within a kinetic-rate equation approach as previously used for charmonia, the formation and dissociation of the $X(3872)$ is controlled by two transport parameters, i.e., its inelastic reaction rate and thermal-equilibrium limit in the evolving hot QCD medium. While the equilibrium limit is controlled by the charm production cross section in primordial nucleon-nucleon collisions (together with the spectra of charm states in the medium), the structure information is encoded in the reaction rate. We study how different scenarios for the rate affect the centrality dependence and transverse-momentum ($p_T$) spectra of the $X(3872)$. Larger reaction rates associated with the loosely bound molecule structure imply that it is formed later in the fireball evolution than the tetraquark and thus its final yields are generally smaller by around a factor of two, which is qualitatively different from most coalescence model calculations to date. The $p_T$ spectra provide further information as the later decoupling time within the molecular scenario leads to harder spectra caused by the blue-shift from the expanding fireball.