If you order from Seller A on "Fulfilled by Amazon", then Amazon will ship you from the nearest warehouse that has the same product, even if it's technically stock of Seller B.
And Seller B might have handed a crate of counterfeits to Amazon. Angering both the customer and Seller A who has no way to actually enforce the quality of what they sell on Amazon.
Pros to comingling:
1. Makes customers happier to get their item sooner
2. You don't need to label your items, which either saves you time or saves you the 20 cents per item fee Amazon charges
3. Your items get processed quicker. If your items are in between warehouses, they can still be "shipped" to the customer.
Cons:
1. Counterfeit possibility. This varies by item. Amazon claims to track which seller inventory was sold from.
2. Bad returns, may hurt your account or require time to deal with.
Basically sometimes it makes sense and sometimes it doesn't. I use a prep center which labels for me, and when I send in items myself I have Amazon label them.