The key difference is in template format. IDKit SDK uses proprietary Innovatrics template format which allows for higher precision and very high 1:N identification speeds. ANSI&ISO SDK uses standardized template format which is compatible with external biometric software but supports only basic 1:1 verification.
As for interoperability between IDKit SDK and ANSI&ISO SDK, both SDKs can create templates in their respective template format from original fingerprint image. IDKit SDK can additionally export templates in format used by ANSI&ISO SDK, but import of ANSI&ISO SDK templates into IDKit SDK is not supported.