In this paper, the governing equations of non-isothermal two-phase flow in unsaturated, deformable porous media are presented based on different representations of the gaseous phase along with their implementations in the open-source FEM code OpenGeoSys 6. As one implementation utilises the Richards equation to represent the unsaturated system whereas the second implementation relies on a two-component two-phase flow formulation, the impact of a free gaseous phase on model predictions is illustrated by a series of tests of increasing complexity, motivated by similar investigations in Task C of the DECOVALEX 2023 project. We demonstrate that the governing equations of both implementations collapse and become identical in fully saturated regions and that the numerical implementations remain stable in the special cases. Furthermore, the implicit assumptions made in the Richards equation are explicitly applied to the physically more complex and comprehensive TH²M model. Thus, the impact of a constant residual gas pressure on the model predictions is investigated. Finally, the examples chosen for this work feature thermal consolidation and pore fluid pressurisation effects in the Opalinus Clay due to heat release from a nuclear waste canister as well as dry-out with subsequent resaturation of a bentonite buffer around the heat source. All test cases are evaluated on the level of the governing equations of each model as well as on the level of results obtained by each model for a discussion of conceptual model uncertainty.