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A projection-based formulation is presented for non-linear model reduction of problems with extreme scale disparity. The approach allows for the selection of an arbitrary, but complete, set of solution variables while preserving the structure of the governing equations. Least-squares-based minimization is leveraged to guarantee symmetrization and discrete consistency with the full-order model (FOM). Two levels of scaling are used to achieve the conditioning required to effectively handle problems with extremely disparate physical phenomena, characterized by extreme stiffness in the system of equations. The formulation -- referred to as model-form preserving least-squares with variable transformation (MP-LSVT) -- provides global stabilization for both implicit and explicit time integration schemes. To achieve computational efficiency, a pivoted QR decomposition is used with oversampling, and adapted to the MP-LSVT method. The framework is demonstrated in representative two- and three-dimensional reacting flow problems, and the MP-LSVT is shown to exhibit improved stability and accuracy over standard projection-based ROM techniques. Physical realizability and local stability are promoted by enforcing limiters in both temperature and species mass fractions. These limiters are demonstrated to be important in eliminating regions of spurious burning, thus enabling the ROMs to provide accurate representations of the heat release rate and flame propagation speed. In the 3D application, it is shown that more than two orders of magnitude acceleration in computational efficiency can be achieved, while also providing reasonable future-state predictions. A key contribution of this work is the development and demonstration of a comprehensive ROM formulation that targets highly challenging multi-scale transport-dominated problems.