If both MCU have the same Thread spec software, you shouldn't have a problem with a mixed platform network. I think the issue is the software versions you are using.
The KW41z public Thread release comes with Thread v1.1 spec.
I'm guessing you are using a beta version for the FRDM-K64F+FRDM-CR20A software that is Thread v1.0 spec.
We are internal testing a Thread v1.1 spec release that will be ready by mid January. Once we launch this software you will be able to have FRDM-K64 border router with FRDM-KW41 devices