You want to be sure that your imputation model is compatible with your analysis model. If you log X in the imputation model but don't log X in your analysis model, your regression estimates will be biased. If you don't plan to log X in analysis, it is typically better not to log X in your imputation model, even if that means some impute values are out of bounds. For details see this paper: https://arxiv.org/abs/1707.05360
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