While playing Aven Colony I've regularly run into issues where a building has a massive commute penalty despite the workers being well within the 9 tunnel range of their residence. Today I've managed to get a situation where I can switch between a working solution and a broken one at will. Please see this album:
Sometimes the workers don't follow the direct tunnel path to their destination and instead come out of the opposite side of the habitat and try to navigate from there, either following a massive route, or going through buildings.