They will be similar, but CMP6GX3M3A1600C8 is newer and could use a different IC. It also has the DHX Pro connector for the Airflow Pro and future accessories.
As a rule, two triple-kits are not guranteed to work together, as they were only tested as triple-kits (3-up). Ideally, for 12GB, you should go for a dedicated 12GB kit, where the modules are all tested together.
That said, you should be okay with two TR3X6G1600C8D kits, though you may need to tweak the QPI/DRAM voltage up a little bit (try the XMP value first though).
