Bigger tyres inherently create more rolling resistance. The reason they can perform better in the real world is because they are the only real source of damping on the bike and because they enable safe use of lower pressures. But as long as you can stay in the operaring window of the narrower tyre, it will perform better than a wider tyre for the same percieved comfort/casing tension. And also it'll be aerodynamically faster and less affected by crosswinds.
Frame flex doesn't measurably affect power transfer, only effect it has is mental and on handling. Too much stiffness, does however worsen the damping ability of the system, slowing you down on rough surfaces, and creates more physical and mental fatigue.
I had a really long post written about why this isn't quite right but I realized that no one really wants to debate tire pressure on here. The summary is that if you approximate by % drop the RR should be the roughly the same, but there is a point above which increasing tire pressure increases RR. This is because a tire is not an ideal spring but follows an S curve, and you can end up with resonance / "impedance" mismatch. Wider tires have greater volume and are a lower pressure for the same % drop--meaning you can often run less % drop and still avoid the "impedance" mismatch condition. This theoretically means a wider tire can be less RR, depending on the surface.
Skin tension is related but is a red herring because it's a derivative (in the math sense) of the volume equation that governs the spring rate of the tire.
Given we are talking about resonance and energy absorption, speed is a key input too. The faster you ride, the greater the chance that, on a rough road, you will enter the zone where a higher pressure results in increased RR.
The same resonance / "impedance" issues should also apply to frames. Still, I don't think anyone has published data to suggest when / where a frame is so stiff this actually happens vs. tires when assuming the frame is totally rigid, so we have no idea if this frame or any other is too stiff other than how it feels to the riders.
