Why is there difference between the "ideal scenario" and the "ideal simulation" for this isolation transformer model?
Because even a simulator needs a bit of reality built in. 

You cannot have isolated nodes in a general simulator, as this introduces singularities in the differential equations. So, to avoid this there are additional simulator parameters that let some measure of reality “creep in” into the simulation. 

In this particular case, it might be “gmin” the minimum conductance between any node and ground. Reduce it, and you will reduce the effect. Reduce it too much, and watch the simulator go singular.