When animating vertices (FFD) all vertices are keyed together. If they weren't, Spine would need a timeline for each vertex (or group of vertices), and that becomes unmanageable.

One feature that can help a little is Key Adjust:
http://esotericsoftware.com/spine-dopesheet#Key-Adjust
This way if you are moving a vertex for a mesh that already has many keys, you can adjust all the keys at once.

Another way to manipulate meshes is to use weights:
http://esotericsoftware.com/spine-weights
This way you can animate the bones and the bones will deform the mesh. If you really wanted, you could have one bone per vertex, but that would be a bit crazy. You can use FFD on top of this to get the exact deform you want, which likely means a lot fewer FFD keys than using FFD alone.