A central challenge in scientific machine learning (ML) is the correct representation of physical systems governed by multi-regime behaviours. In these scenarios, standard data analysis techniques often fail to capture the nature of the data, as the system's response varies significantly across the state space due to its stochasticity and the different physical regimes. Uncertainty quantification (UQ) should thus not be viewed merely as a safety assessment, but as a support to the learning task itself, guiding the model to internalise the behaviour of the data. We address this by focusing on the Critical Heat Flux (CHF) benchmark and dataset presented by the OECD/NEA Expert Group on Reactor Systems Multi-Physics. This case study represents a test for scientific ML due to the non-linear dependence of CHF on the inputs and the existence of distinct microscopic physical regimes. These regimes exhibit diverse statistical profiles, a complexity that requires UQ techniques to internalise the data behaviour and ensure reliable predictions. In this work, we conduct a comparative analysis of UQ methodologies to determine their impact on physical representation. We contrast post-hoc methods, specifically conformal prediction, against end-to-end coverage-oriented pipelines, including (Bayesian) heteroscedastic regression and quality-driven losses. These approaches treat uncertainty not as a final metric, but as an active component of the optimisation process, modelling the prediction and its behaviour simultaneously. We show that while post-hoc methods ensure statistical calibration, coverage-oriented learning effectively reshapes the model's representation to match the complex physical regimes. The result is a model that delivers not only high predictive accuracy but also a physically consistent uncertainty estimation that adapts dynamically to the intrinsic variability of the CHF.