OK, looks like I'm on the right track at least.
I've finally had success building the project at least. There were a large number of undefined symbol errors popping up. For anyone else trying to accomplish this, the end device libraries for thread and 802.15.4 are different for the two projects. Copy the 801.15.4_mac_thrrfd_cm0 and _thread_ed_cm0 libraries from the low power end device project into the libs directory of the hybrid project and change the included libraries to match the new library file names in the project settings C/C++ Build -> Settings -> MCU Linker ->Libraries.