Honestly, I don't see much difference other than his preference in record-keeping. I'm pretty OCD about my records being a *certain* way.
Let's say you have litter A (bred from Doe A and Buck X) and litter B (bred from Doe B and buck X)
2 does from A (AD1 and AD2) and 2 bucks from B (BB1 and BB2). He breeds AD1 to BB1 and AD2 to BB2. All kits are related to Buck X from both parents and both doe A and Doe B (once from each parent).
BUT now let's say you have litter A (bred from Doe A and Buck X) and litter B (bred from Doe B and buck X)
2 does, one from each litter (AD1 and BD1) and 2 bucks, one from each litter (AB1 and BB1). He breeds AD1 to AB1 and BD1 to BB1. All kits are related to Buck X from both parents and both doe A and Doe B (once from each parent). Only now he has the choice to breed AB1 to AD1 which results in grandparents only being Buck X and Doe A or doing the same with B. He can do it but it's not the best choice if he wants to work on a pedigree as that is breeding brother to sister twice.
Personally I prefer the first option as it seems slightly easier to follow because he KNOWS all of his received does are from doe A and all of his bucks are from doe B. But he may find the other way easier and might not care about inbreeding.