It wouldn't bother me, I like to think that I'd understand that he was doing what he needed to do, but I think you'll find that it would bother a LOT of women.
If you think about it, you have the men's toilets - which tend to stink and in which his little girls are likely to see men weeing. You have a situation there where a man is standing there with his penis out and in walk a couple of little girls. How is he going to feel? How is the dad going to feel?
otoh, you have a man going into the ladies. Where he will see...cubicles. Where the children will see...cubicles. And maybe a woman washing her hands.
I know which I think is better.
Perhaps a yell from the doorway? "Bringing my very young daughters in"
Really though, there ought to be mens, womens, disabled and family toilets. (family toilets being a larger space, a single toilet and also where the baby change is located). This is a common problem. Woman with young boys/man with young girls/changing table in the disabled toilet.
It won't happen though, because it costs money and takes space.