In engineering design research different models of functional decomposition are advanced side-by-side. In this paper I explain and validate this co-existence of models in terms of the Kuhnian thesis of methodological incommensurability. I advance this analysis in terms of the thesis’ construal of (non-algorithmic) theory choice in terms of values, expanding this notion to the engineering domain. I further argue that the (by some) implicated threat of the thesis to rational theory choice has no force in the functional decomposition case: co-existence of different models of functional decomposition is rational from an instrumental point of view. My explanation covers cases in which different models are advanced as means for the same objective. Such cases cannot be explicated with the explanatory construct of variety in objectives, as advanced in other analyses of co-existing conceptualizations in engineering.