I think what you are suggesting is aligned with my proposal to make miners pay in proportion to their block size.
The existence of empty blocks doesn’t necessarily bring down average throughput because they are balanced out by full blocks. However, if these oscillations continue (as I believe they are likely to),1559 is not making fees predictable for average price-sensitive users. That would mean we are incurring the costs of incentive misalignment without getting much out of it.