Yes, it is practically about Vanitas "absorbing"/enslaving Ventus' heart which is also a part of their final battles.
This is even reflected in the actions and dialogue in both Ventus' and Aqua's scenario, as Vanitas insists on completing their union/fusion not only because it would complete the X-blade (and that was the primary reason), it is also to firmly fuse his and Ventus' heart together (with him in control of course).
You have to remember that although both Ventus and Vanitas have each their own hearts (Vanitas' being a relatively newborn one), they originate from the same heart and at the core of Vanitas' heart is a shard that originally was part of Ventus' heart.
This is also why Ventus says this:
I've got a better idea. How 'bout I destroy you both?
If you want to take it really specific you could even compare it to Ansem SoD possessing Riku in KH 1 and to Master Xehanort possessing Terra.
The only difference is that in these two cases the hearts involved were of different origin to begin with while in Ven's/Vanitas' case one of the hearts was born from the other originally.