I believe this is due to some overzealous standardization step in the automated processing pipeline (boolean vectors are converted to numerical vectors for processing). You can disable that using the "Minimal" feature extraction:
data = {True, True, False, True, True, True} -> {False, True, False, True, False, False};
cf1 = Classify[data, Method -> "NaiveBayes"];
cf2 = Classify[data, Method -> "NaiveBayes", FeatureExtractor -> "Minimal"];
cf1[{True, False}, "Probabilities"]
(* {<|False -> 0.30733, True -> 0.69267|>, <|False -> 0.963594, True -> 0.0364056|>} *)
cf2[{True, False}, "Probabilities"]
(* {<|False -> 0.579921, True -> 0.420079|>, <|False -> 0.579921, True -> 0.420079|>} *)