Hi Yosuke,
Thanks for your very detailed explanation of your question! The MCALT template/atlas boundaries are not intended to match MNI. This is essentially a full replacement for MNI space for use with older brains. If you are using MCALT with SPM, then you should use the MCALT TPM's, and SPM can then normalize images to MCALT space rather than MNI. Atlases that were designed in MNI space are not compatible with MCALT without transforming them first somehow to match the new space.

Does that help?
Best,
Chris