Stray-inductance and capacitance of non-isolated heat-sink
If you have a heat sink flailing around with hundreds of KHz square waves on it at hundreds of volts, you've got an EMI source. Since usually the drain of a MOSFET is common with the heatsink when not isolated, that's typically going to maximize the pain. 

If the case is quite conductive, capacitive coupling to the outside world can be minimized but there will still be some circulating currents to deal with internally. 

Magnetic coupling isn't usually a big problem with good design (minimize loop area in current-carrying loops). 

Good thermal coupling, low noise, and isolation tend to be at cross-purposes.