How do diffusers turn velocity into pressure? There are many resources that give explanations for the behavior of nozzles and diffusers. But at the crux point they all say, "Velocity goes down and pressure goes up." As if that doesn't warrant any deeper explanation, or as if it were just a law of nature.

To me, the reason behind this energy transfer isn't obvious.

To maintain a constant mass flow rate, $\dot{m}=const$ , through a small inlet and a large outlet you would need a deceleration of the flow. To decelerate a flow requires a force, $F=ma$. Forces interactions are equal and opposite so the fluid would exert a larger force, relative to the inlet, if forced to slow down. But what is the origin of this decelerating force? Why does this geometry increase the $\frac{F}{A}$ of the molecules that pass through it? I understand the energy conservation, but how is this behavior explained in terms of force interactions?

It's like you asked how an electric motor worked and someone said, "By turning electric energy into rotational motion." and you said, "How?" And they just repeat, "By turning electric energy into rotational motion." Energy balance just isn't descriptive enough.
While we wait for a probably better answer, here's my tentative.

You state that you understand the concept of constant mass flow. Let's for a moment write the mass flow properly:

$$\dot{m} = \rho A v$$

on the left we have the mass flow $\dot{m}$, on the right we have the density $\rho$, the area $A$, and the velocity $v$.

If we want $\dot{m}$ to be constant while changing $A$, we need to change $\rho$ and $v$ accordingly. In these scenarios $\rho$ is taken as roughly constant, leaving only the velocity as free variable. While this might be more true for liquids, it is not too far from the reality also when air is involved (although you might observe minor variations in density).

Where do the forces come from? The walls of the duct and the fluid downstream (when decelerating, the fluid that is already at a slower speed will effectively work as a "wall" for the incoming fluid) or the fluid upstream (when accelerating the incoming fluid will push the rest of the fluid like an extruding piston).

In other terms the required energy comes from the pressure differential (the faster fluid has lower pressure).