Does enabling or disabling bitcode would affect the existing features of the app in any way ?
For eg: If I choose to untick the option "Rebuild from bitcode" while sharing the ipa to QA team and on the other hand If I chose to enable bitcode when I am uploading the app to AppStore.
Is there any possibility that the some test cases might go live untested ?
By testing with bitcode compilation enabled, plus exporting all app variants and testing those, you'll have more thorough coverage of the real scenarios that your end users will encounter in the App Store download. We recently updated our documentation for testing builds like your user will receive, and it includes this guidance.