What you may be getting confused about is the "ideal transformer" in the equivalent circuit. You should not regard it as having any magnetic qualities at all. Try and see it like this: -
Whatever voltage you have on the input to the ideal transformer, \$V_P\$ is converted to \$V_S\$ on the output of this "theoretical" and perfect device. It converts power in to power out without loss or degradation such that: -
\$V_P\cdot I_P = V_S\cdot I_S\$
The ratio of \$V_P\$ to \$V_S\$ happens to be also called the turns ratio and almost quite literally it is on an unloaded transformer because there will be no volt-drop across R3 and L3 and only the tiniest of volt-drops on R1 and L1.
This means you now have a relatively easy way of constructing scenarios of load effects and recognizing the volt drops across the leakage components that are present.
The equivalent circuit of the transformer is really quite good once you accept that the ideal power converter is "untouchable" and should just be regarded as a black box. For instance you can measure both R1 and R3 and, by shorting the secondary you can get a pretty good idea what L3 and L1 are. With open circuit secondary you can measure the current into the primary and get a pretty good idea what \$L_M\$ is too.
I think your confusion lies in your first assumption. An ideal transformer doesn't even have windings, because it can't exist. Thus, it doesn't make sense to consider inductance, or leakage, or less than perfect coupling. All of these issues don't exist. An ideal transformer simply multiplies impedances by some constant. Power in will equal power out exactly, but the voltage:current ratio will be altered according to the turns ratio of the transformer.
For example, it is impossible to measure any difference between a 50Ω resistor, and a 12.5Ω resistor seen through an ideal transformer with a 2:1 turns ratio. This holds true for any load, including complex impedances.
simulate this circuit – Schematic created using CircuitLab
Since an ideal transformer can't be realized, considering how it might work is a logical dead-end. It doesn't have to work because it is a purely theoretical concept used to simplify calculations.
The language you used in your first assumption is a description of the limiting case that defines an ideal transformer. Consider a simple transformer equivalent circuit:
simulate this circuit
Of course, we can make a more complicated equivalent circuit according to how accurately we wish to model the non-ideal effects of a real transformer, but this one will do to illustrate the point. Remember also that XFMR1 represents an ideal transformer.
As the real transformer's winding resistance approaches zero, then R2 approaches 0Ω. In the limiting case of an ideal transformer where there is no winding resistance, then we can replace R2 with a short.
Likewise, as the leakage inductance approaches zero, L2 approaches 0H, and can be replaced with a short in the limiting case.
As the primary inductance approaches infinity, we can replace L1 with an open in the limiting case.
And so it goes for all the non-ideal effects we might model in a transformer. The ideal transformer has an infinitely large core that never saturates. As such, the ideal transformer even works at DC. The ideal transformer's windings have no distributed capacitance. And so on. After you've hit these limits (or in practice, approached them sufficiently close for your application for their effects to become negligible), you are left with just the ideal transformer, XFMR1.
Best Answer
It seems to me that you have to be helped to recognize this: -
Picture from here.
In other words, if you apply 1 volt to the blue winding then 1 volt will appear on the red winding. This happens when the turns on both windings are in-phase and very closely coupled but I haven't given a proper reason why this happens yet.
Consider ONLY the blue winding that has 1 volt applied to it. The current into that winding is the magnetization current and, it ramps upwards governed by: -
$$\dfrac{di}{dt} = \dfrac{V}{L}$$
In that blue winding there is a back-emf that is equal to the applied voltage. This is an induced voltage and, if you introduced the red winding (the secondary) you would see the same induced voltage. It would be the same because the magnetic flux produced by the magnetization current in the blue winding is fully coupled to the red secondary winding.
Now what would happen if we attached a load resistor of 1 ohm to the secondary winding?
Current (1 amp) would flow into that 1 ohm resistor like so: -
That current (on the face of it) could create an extra magnetic flux in the transformer windings. The extra flux might (possibly) do two things. It might: -
If it caused the output voltage to rise then we would have an unstable situation because, due to that voltage increase, there has to be more current flowing into the 1 ohm resistor and this means more flux and more voltage and this ends in disaster.
If it caused the output voltage to fall then the back emf in the primary would also fall and we would have a situation where the primary took an unholy amount of current.
But, the reality is that neither of the above happens. If either of the above happened we end with contradictions - if the secondary voltage rose driving more current through the 1 ohm load, the primary voltage also has to rise but it can't because, it is limited by the applied 1 volt hence, current has to simultaneously flow back into the 1 volt source on the blue winding whilst also flowing into the secondary load i.e. we have uncontrolled perpetual energy that self-destructs.
If the secondary voltage fell we have the contradiction of primary (blue) current rising uncontrollably which means flux rises uncontrollably which means secondary (red) voltage has to rise - a contradiction.
The sensible equilibrium is found when we examine the 3rd scenario: -
This can only happen when the load current flowing from the secondary (red) is matched by a load current flowing into the primary (blue). These load currents produce equal and opposite magnetic fluxes and hence they cancel leaving the original magnetization flux and, that magnetization flux carries on doing what it did all along - setting the output voltage to be equal to the input voltage (1:1).
For a transformer with a non unity turns ratio, the secondary load ampere-turns are equal and opposite with the primary current ampere-turns that flow due to the load.