I agree with all your points. I suspect your guess for the probability of cage-free systems being better than furnished cages is lower than my guess of 2⁄3. However, I do not think this matters much. In practice, I would still generally prioritise research on decreasing the uncertainty over cage-free egg campaigns.
As I say in the post, I think that the WFI analysis does not include some potentially significant harms (such as chronic stress/pain from violence or parasites—which are likely higher in cage-free systems).
It also excludes foot lesions and air quality, which are discussed in section “Important Consideration” of Chapter 9 of the book Quantifying Pain in Laying Hens by Cynthia Schuck-Paim and Wladimir Alonso from WFI. Here are their conclusions.
[...] the reporting of the relatively low incidence of the more severe and painful manifestations [of foot lesions] in layers [16,21–23] makes it unlikely that consideration of this harm would affect the estimates substantially to the point of changing any of the conclusions.
[...]
[...] it is not unreasonable to suppose that through the potentially detrimental effect on the respiratory system [24] and on mucous membranes, high concentrations of ammonia can lead to a prolonged state of discomfort [26]. This is an important welfare concern, which is likely to increase the estimated time in pain endured in cage-free facilities, depending on the prevalence of (cage and cage-free) facilities where manure is not regularly removed and the ventilation flow is insufficient, and on the time endured in discomfort (e.g. in temperate regions, higher levels of ammonia in cage-free relative to cage housing have been found in winter, but not in summer [27,28]).
I agree with all your points. I suspect your guess for the probability of cage-free systems being better than furnished cages is lower than my guess of 2⁄3. However, I do not think this matters much. In practice, I would still generally prioritise research on decreasing the uncertainty over cage-free egg campaigns.
It also excludes foot lesions and air quality, which are discussed in section “Important Consideration” of Chapter 9 of the book Quantifying Pain in Laying Hens by Cynthia Schuck-Paim and Wladimir Alonso from WFI. Here are their conclusions.