Is this restricted somehow to Mac App Store applications?

Is a warning issued as stripping native commands  may break application 

Is it not possible for the user to provide their own Info.plist with  a 
different bundle identifier that doesn’t collide?

I’m not real familiar with the build process. But would it be possible for the 
user to build their own jdk that substitutes something else for the colliding 
identifier that gets embedded?

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