Gravitational instabilities exert a crucial role on the Earth dynamics and in particular on its differentiation. The Earth's crust can be considered as a multilayered fluid with different densities and viscosities, which may become unstable in particular with variations in temperature. With the specific aim to quantify crustal scale polydiapiric instabilities, we test here two codes, JADIM and OpenFOAM, which use a volume-of-fluid (VOF) method without interface reconstruction, and compare them with the geodynamics community code ASPECT, which uses a tracking algorithm based on compositional fields. The VOF method is well-known to preserve strongly deforming interfaces. Both JADIM and OpenFOAM are first tested against documented two and three-layer Rayleigh-Taylor instability configurations in 2-D and 3-D. 2-D and 3-D results show diapiric growth rates that fit the analytical theory and are found to be slightly more accurate than those obtained with ASPECT. We subsequently compare the results from VOF simulations with previously published Rayleigh-Benard analogue and numerical experiments. We show that the VOF method is a robust method adapted to the study of diapirism and convection in the Earth's crust, although it is not computationally as fast as ASPECT. OpenFOAM is found to run faster than, and conserve mass as well as JADIM. Finally, we provide a preliminary application to the polydiapiric dynamics of the orogenic crust of Naxos Island (Greece) at about 16 Myr, and propose a two-stages scenario of convection and diapirism. The timing and dimensions of the modelled gravitational instabilities not only corroborate previous estimates of timing and dimensions associated to the dynamics of this hot crustal domain, but also bring preliminary insight on its rheological and tectonic contexts.