Does Clear Data on App Settings clears all Android KeyStore stored for that certain app?

Clear Data in App's Setting will clear only the data, created / generated run-time by user. Like, preferences, database etc.

It will not clear data, stored at the time of app building

clears all Android Keystore stored in that certain app? Or it leaves certain bits of data?

Yes, It will reset all data of that application.

Clearing the data, however, will remove any user data, databases, etc -- this includes things like account settings, persistent preferences, etc.

Clearing the data should revert the application back to it's state as it was when you first installed it.

As an example, assume we have a Twitter application. Clearing the data would remove any information at all, including your login information, who you're following, whether or not you want to be notified of new tweets, and things like that.

In short, it delete all applications data.

Check description for more details