Can a normally poorly handling airframe with high moments of inertia actually have superior flight dynamics under autonomous control?
The underlying assumption of your question seems to be that a higher control bandwidth always leads to better disturbance suppression. Since a higher control bandwidth is easier to achieve with low-inertia systems, aircraft with low inertia would have better disturbance suppression.
This assumption can work in theory, especially for SISO (single-input, single-output) systems. However, for aircraft, we are essentially dealing with MIMO systems. While we can achieve near-perfect disturbance suppression for one degree of freedom (e.g., zero variation in altitude), this will inevitably lead to large excursions of other degrees of freedom. For example, disturbance suppression in altitude will lead to large variations in pitch as we try and keep AoA constant with every gust. So, for a MIMO system like an aircraft, we have no choice but to formulate a cost function of what we consider a 'smooth' ride, and balance the control scheme across various degrees of freedom.
Since we are considering a balancing act, it then makes sense to tune the internal dynamics of the aircraft such that a smooth ride is naturally achieved. So that means: high inertia for degrees of freedom experienced by the passenger, and low inertia for degrees of freedom not felt by the passenger. In practice: larger fuselage inertia and smaller control surface inertia.
Unsurprisingly, this is how it works in practice: larger aircraft are generally more comfortable, whereas at the same time, degrees of freedom not felt by the passengers are exploited in modern aircraft for gust suppression. For example, wings are more and more dynamically decoupled from the fuselage by highly flexible composite wings. Ailerons are split in smaller sections for gust suppression, you may find videos of &quot;dance of the ailerons&quot; for modern aircraft.