This issue has been resolved. the issue had occurred because of the Adobe target extension has option called GDPR opt in enabled / disabled which conflicts with adobe opt in permission in our case. Earlier it set to enabled but later on when it disabled all working as expected. I 've report this with Adobe.
Thanks for the response. I've had check I can see the correct values return by 'adobe.optIn.permissions' for each category like below but it can also shows the warning message
where as when I interacted with my cookie banner and select only allow Target cookies then with my earlier implementation (in question) works correctly and I can see the experience through target and interestingly can't see the above target warning
Please set 'Is Opt In storage enabled' to 'Yes' (Launch > EC ID service extension) so as to store the opt in permissions in a first party cookie 'adobeujs-optin'. You can also debug in the browser console to see 'adobe.optIn.permissions' returns the expected result of each category or not.