I can't find any information that multiple simultaneous cue points isn't supported but trying to add two cue point at the same time code in Adobe Media Encoder gives an error – indicating that you should probably avoid it.
Another solution would be to collect all the transformations for a given keyframe and collect them in the parameter list for a single cue point. An example could be:
layerChangeCue
layer1
:"x:123;y:456;s:0.78"
- ⋮
layer4
:"x:123;y:456;s:0.78"