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I agree that :bypass option is a kind of hack, but you have to have such a permission to do that so you don't use it accidentally.
Unfortunately our requirement is to automate the update a version number in the AssemblyInfo files, and check them into MKS before the build. Since the builds are often done many times a day it would be quite time consuming to manually have to accept the change packages and will as such add a manual process into what should be an automated build. I get the point of not having too many options for the plugin on Jenkins so that it's not overly complicated but perhaps my argument can convience you to reconsider adding the bypass option to the check-in plugin. Or perhaps you have other suggestions how can we automate the check-in of AssemblyInfo files changed by the builds in Jenkins?