I'm not a biologist.
From a chemist's point of view, these molecules should have similar polarity. Their structure is very similar, actually.
Considering your replacement rule is correct, I would say there wouldn't be much effect other than observing different colors. What is also plausible is that you'd have to reverse the interpretation of your results, e.g. methylene blue stains X, but crystal violet stains Y whereas carbol fuchsin stains Y and safranine stains X.
Was that clear?
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