Why is ground shared between primary and secondary side in LT3750 circuit example
The simple answer is that is a just an example circuit.

LTSpice needs you to have ground path for each node, easiest way to do this is put the standard grounds on both sides.

To simulate isolated grounds, put a very large (1,000,000,000 ohms or so) resistor and a very small (1 pico farad) capacitor in parallel. This gives you an isolated ground as you would have in real life. The LT Test Fixtures don't bother with this to keep the diagram clearer, and to make the simulation output nice and clear.

Obviously you will then have to give a label to the isolated ground, and measuring the voltage relevant to the isolated ground will require putting an equation in the simulation output to make the voltage you're interested relevant to the ground you are interested in.