How does the experience of "realisation of Sunyata" differ from "realisation of Anatta"? In what ways does the experience of "realisation of Sunyata" differ from the experience of "realisation of Anatta", for the practitioner?

The two aims are apparently non confirming, as far as I know, at least that is what their respective schools believe.

So in what ways does choosing one ideal over the other lead to a  difference in experience for the practitioner?
There is no difference between anatta &amp; sunnata in terms of realisation. If there was a difference then the Anatta-Lakkhana Sutta would be a lie &amp; false because the five arahants in that sutta would not really be arahants (fully enlightened). They would only be partially enlightened. 

The definitions of anatta &amp; sunnata in the Pali suttas are basically identical, namely: 


  Therefore, surely, O monks, whatever form, past, future or present, internal or external, coarse or fine, low or lofty, far or near, all that form must be regarded with proper wisdom, according to reality, thus: 'This is not mine, this I am not, this is not my self.'
  
  Anatta-Lakkhana Sutta
  
  
  
  And what is the emptiness mind-release? There is the case where a monk, having gone into the wilderness, to the root of a tree, or into an empty dwelling, considers this: 'This is empty of self or of anything pertaining to self.'
  
  MN 43
  
  


In terms of the teachings, anatta &amp; sunnata are different because anatta was taught 1st, in the 2nd sermon of the Buddha, where a gradual sermon was given that associated anatta with anicca (impermanence). Here, it was reasoned because something is impermanent &amp; subject to disease, it cannot be a 'self' or regard as 'mine' ('belonging to self'). When the minds of the listeners penetrated this reality, the self-views in the mind dissolved, which was enlightenment. (In addition, the teaching of 'dukkha' also helped extinguished the defilements, such as craving). 

As for sunnata, it does not rely on impermanence because it simply, correctly &amp; directly asserts there is no self within the five aggregates. This is easily observed in meditation. For example, observing the breathing itself or a body part or observing sense consciousness itself, in can be seen easily there is no 'self' in the breathing or in a finger or in sense consciousness; just as it can be seen easily there is no 'self' in a rock, tree or cloud.  

In conclusion, anatta was a gradual teaching for beginners that used impermanence (anicca) to assist in the realisation. However, when the realisation itself occurs, there is no difference from sunnata.