Bundle Identifiers are unique in Apple ecosystem. You want to have an enterprise distrubition of app. Apple guidelines
https://developer.apple.com/library/content/documentation/IDEs/Conceptual/AppDistributionGuide/DistributingEnterpriseProgramApps/DistributingEnterpriseProgramApps.html
Once you have the write provisional profile and new bundle identifier for enterprise deployment. you need to put new AppId to config.xml and build your iOS app. This way AppStore and Enterprise version of your apps willhave 2 different bundle identifiers and can be installed on same device.
Possibly you will want to automate this build process .
you can read how to create ipa file on here
How can I deploy (create .ipa) iphone app using 'cordova build ios --release'?
i would extend cordova build system and have
cordova build ios --release
// app store release
cordova build ios --enterprise-release
// enterprise release