The same question can be asked for any sealant or sealer. Improper installation is a problem for anything.
RTV does not pass water. If it does the application is not correct which is really the first question
A good quality of RTV is it is not permanent. This sealant does hold well, it is not a "permanent" type of adhesive that is meant to joint parts together on a permanent basis. It is a sealer not an adhesive.
Clean up is done with physical scraping and/or using a chemical like rubbing alcohol, acetone, brake/carb cleaner, or WD-40
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