First, the impedance of a simple half-wave dipole antenna is 73 ohms, not 50 ohms. Furthermore, the parasitic elements D1/D2 and RE in different half-wave antenna designs can affect the impedance of the DE unit, ultimately achieving the desired impedance value, such as the common 50 ohms, or the low impedance 12.5 ohms, or the 100 ohms used in large full-length antennas. In summary, you cannot measure it this way.
Furthermore, the Yagi antenna requires a balanced transmission line. Using mmana-gal to simulate this situation will not work correctly. The toroidal choke serves to eliminate common-mode currents, and this will not affect your impedance matching. Undesirable common-mode currents can lead to radiation from the feedline, which negatively impacts the direction of the radiated signal.