The openthread is pre-compiled in order to get started without much fuzz. If you would like to modify it, please refer to the "Building the latest OpenThread libraries" guide. One hint is to use the same release commit that was used in the SDK. The tag is mentioned in SDK\external\openthread\project\readme.txt. If you do this, the library should be API compatible with the one used in the Thread and Zigbee SDK version that you are using.
