It's just a computer formula that gives us an idea of how the playoff picture would play out .. it's far from an exact science.
If the tool says those 5 programs would all be within a close percentage of each other if they all won out, i would look at that as "the playoff committee would have a tough decision to make" in other words don't look at the data so precisely .. use it to get more of a relative sense of how things are going to play out. And i'm not sure the playoff committee would move any 1 loss team ahead of ND if all of those 5 teams won out. the cache of a 12-0 record still holds a lot more weight than the playoff predictor tool is giving it credit for.
the good news is ND has a couple of really easy games the final 2 weeks (Syracuse is way overrated like much of the other ranked teams ND has played this season) so their chance of winning out is statistically higher than much of their competition. ND is in a really good position right now (a lot of external factors is on their side).