MOSFET Common Source Output Analysis
Yes, there is a huge difference between those two circuits. When the output voltage is taken from the source terminal we have a Source Follower (common-drain amplifier). The Output voltage is Vgs lower than the voltage at the MOSFET Gate. The voltage gain is less than one (\$A_V = \frac{R_4}{\frac{1}{gm} + R_4}\$) and Rout is 1/gm (low).

The second circuit is a classic Common Source with Source Degeneration resistor (R4). The voltage gain is equal to \$A_V = -\frac{R3}{R4+ \frac{1}{gm}}\$ 

The voltage gain is negative but usually, we ignore this "minus" sign. Because this only informs us about 180-degree phase shift between Vin and Vout. When the voltage at the MOSFET Gate increases, the drain current also increases. The current in the drain resistor (R3) increases (ID = IR3) which increases the voltage drop across it (across R3, VR3 = IdR3) so the drain voltage decreases (Vd = Vdd - IdR3) which is 180 degrees to the change in gate voltage. And the output resistance is Rout = R3.