V1 and V2 are referred as cloaks. KCM1, KCM2 and KM are modes.
My theory is this;
1. Kyuubi Modes are ninjutsu while,
Tailed beast V1/V2 Cloaks aren't ninjutsu or Better put are not ninja skills.
2. Kyuubi chakra Modes is Naruto having a dominant and specific control over the Kyuubi's power. The Kyuubi's red chakra is turned yellow (like Naruto's chakra) showing Naruto's full control of it.
With Chakra cloaks, the dominant control goes to Kurama with Naruto having less.