How you manage to find your father in that vault is NOT important. In talking with him, he thought he missed a lot, but as far as I figure, he basically just missed the step of the quest where you go to the jefferson memorial to check out project purity. It's the same thing I had happen to me after I finished strictly business. I went to talk to Eulogy or whatever his name is... ended up buying the kids freedom... hadn't even found lamplight on my map, or received the rescue from paradise quest, but I'd completed the mission apparently. No harm, no foul. Just because there are multiple ways to accomplish something doesn't mean it's broken.
I suppose what the GS employee told me is kind of true. You can leave Vault 101, run over to the garage, and find dad in Vault 112 in 3 minutes, but it won't really make a difference... just because you didn't follow *every* step of the quests designed to help you find him doesn't mean you didn't find a way to accomplish your end goal.