Would denoting if a seller under FBA is using the commingling service help solve this issue, or would that negatively effect the benefits Amazon reaps from this type of inventory model?
Exposing which FBA sellers commingled would lead to avoidance of those sellers by quality conscious consumers, which would lead to more opting out, which would drive up costs and prices on Amazon. Preference for commingling is a deliberate choice by Amazon that consumer transparency on sourcing and avoiding fraud is less important than minimizing prices.
A seller can opt out of comingling, but it costs the seller money. I assume amazon calculated the increase cost of the inventory control and pasts those cost on, so it won't drive down Amazon's profit.
Since Amazon doesnt label which seller opts out, it doesn't give much incentive to do it.