Carbon fibre composites owe their exceptional mechanical properties to the characteristics of their constituents; fibres and resin. However, uncertainty in these individual constituent properties can introduce significant variations in the macroscale mechanical performance of composites. These variations are amplified in the presence of various plies in the composite and pose a challenge to quantify during manufacturing stages. In this study, uncertain constituent material properties are propagated to the macroscale composite through multiscale homogenisation to compute the varied resultant thin-shell stiffness matrices. An in-house-built automated simulation environment has been used to create a physics-conforming trainable database for model training, testing, validation and uncertainty quantification using Gaussian Process Regression (GPR), Artificial Neural Networks (ANNs), and Multiple Linear Regression (MLR). Through rigorous comparative analyses, the superior performance of GPR is demonstrated when compared to alternative techniques with R² ≥ 0.99 and NRMSE < 10⁻⁷. Further, the findings approve the validity of GPR for extrapolatory predictions. For instance, a randomly sampled [-5, 5] % variation of constituent material properties leads to extreme uncertainties in macroscale ± 0.067 %, for axial stiffness with excellent GPR predictive accuracy of R² = 0.99. This slightly increases to ± 0.14 % for a variation of [-10, 10] %. Moreover, the extreme uncertainties indicate that the direct axial and bending stiffnesses are more sensitive to variations in constituent properties than others. Additional investigations presented in the paper produce predictive models and uncertainty bounds for all stiffness entries that are of high importance for macroscale property control during manufacturing.