I think it might be in case they get a seed in their throat and cough.

But I always gave my children multigrain bread, I didn't want them developing a taste for white bread. I don't eat it anymore - I find it gives me a tummyache. And DS actually prefers "seed bread" and if either he or DD have white bread they seem to get a mini sugar high from it.

Re the digesting of the wholegrains - nobody does, it's not just babies that can't. If you checked out your own poo you'd find the seeds in there too. That's why it's so good for you, the roughage cleans out the intestine.