If company 2 had published their work, then it would count as prior art. The benefit of first-to-file is that there's no more expensive discovery to go through inventors' lab notebooks or other things to try to establish the definitive date when someone "invented" something. Instead, this gets reduced to checking a publication date, which should be a matter of public record. That reduces litigation costs. It also encourages people to publish their research. Both of those are good things.