Primary and secondary currents of a transformer driven with clock pulse
Magnetizing inductance is in parallel with the perfect transformer model, not in series. Series inductance represents leakage inductance ie inductance that does not contribute to the magnetic field applied to the secondary winding..

Maybe you should try modelling both for a decent representation of reality. Then add on copper losses as series resistors and eddy current losses as a resistor in parallel with the primary. You should also consider self resonances due to interwinding capacitance.

Only then will you get a fair representation of reality.

Ignoring all the little effects of adding series and parallel resistance, inductance and capacitance, when you have 50:50 square wave going through a transformer you can forget about the DC content; the output will have an average value that is zero so, if the mark-space ratio were 10%, the output waveform would peak at 90% for 10% of the time and remain at -10% for 90% of the time. 

If you need this to be tied to 0V so that at any reasonable MS ratio, the output voltage was clamped to round about 0V you'll need a series capacitor and a diode clamp to 0V. Now for a broad range of MS ratios, the peak voltage will be Vpk-Vdiode and the low voltage will be -Vdiode. Hope this helps.