Flow matching enables likelihood-free training, yet alignment methods increasingly reuse conditional flow matching (CFM) losses as endpoint negative log-likelihoods (NLLs) and their old/new differences as log-likelihood ratios. We characterize when these substitutions are valid. For linear Gaussian paths, we exactly decompose endpoint NLL into entropy, a weighted CFM objective, an interior velocity--score residual, and a boundary residual. Thus CFM-only estimates and differences are exact only when the corresponding residuals cancel. At the off-policy population optimum, ordinary CFM is not generally a pointwise NLL estimator, whereas \(w_{\mathrm{sc}}(t)=(1-t)/t\) removes the interior residual; this positive result does not extend generally to training or on-policy alignment. On-policy log-ratios can remain biased even for identical endpoint laws or after surrogate optimization. Experiments across dimensions, distributions, and geometries support these conclusions and the mechanisms that make inexact ratios useful. **More broadly, the decomposition provides a theoretical basis for adapting likelihood-based LLM methods to flow matching, while distinguishing exact substitutions from controlled surrogates.**

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