Well, I've managed to build with Gradle, where Urho3D and other dependencies of my project are built in a separate module, then my project builds as a module depending on the first one. I can just build with a standalone toolchain, but that requires me to create a separate toolchain for every ABI, armeabi-v7a, armeabi-v8, x86...etc, then build and then copy the output shared libraries somewhere where my project can find them, but linking to a different version depending on the main project ABI....and I don't like doing things manually when building.
I can confirm Urho3D builds successfully with the $ANDROID_SDK/ndk-bundle/build/cmake/android.toolchain.cmake, you only have to patch ThirdParty/ik/src/platform/linux/backtrace_linux.cpp to remove the execinfo include.
Also, I found out the reason why the libraries are not included in the APK - when Gradle runs CMake, it sets CMAKE_LIBRARY_OUTPUT_DIRECTORY to app/build/intermediates/cmake/debug/obj/armeabi-v7a (depending on the ABI) and expects to find the .so there. If you change CMAKE_LIBRARY_OUTPUT_DIRECTORY like I usually do, it won't even warn you about it and just proceed.