When finding the EMF induced in an inductor due to both self-inductance and mutual inductance, the EMFs due to both of these contributions are summed. However, I have doubts regarding their summation.
The self-induced EMF is equal to the negative of the change in the net magnetic flux passing through the inductor, which is proportional to the rate of change of the current in its windings. When there is mutual induction in addition to self-induction, then the flux through the inductor changes, which also changes the current in the inductor windings. Considering these facts, I do not see why the net flux through the inductor doesn't equal the self induced EMF.