Clarke transform of pwm signals
The outcomes of the Clarke transform are correct. The alpha component corresponds directly to the \$u_a\$ voltage and the beta component corresponds to the line-to-line voltage \$u_{bc}\$ scaled by the factor \$\frac{1}{\sqrt{3}}\$. This is also answer to the second part of the question because the line-to-line voltage of the voltage source inverter has different shape than the phase voltage.