I am in a similar boat with regard to the commuting and how it works into a training schedule. Basically I just decided to accept the fact that it's an unchangeable part of my schedule and try not to worry about it. Maybe at higher levels of training it would have more impact but at a lower level just count it as miles on the bike and don't sweat it. Maybe just go slow and easy if it's supposed to be a recovery day (easier said than done, I know).