If companies would consistently allow hours other than 9ish to 5ish, so that workers can commute outside of the morning or evening rush hours, then there is plenty of much less expensive housing available a ferry ride plus a short drive from Seattle over on the other side of Puget Sound.
If you have to travel to Seattle during the morning rush or home from Seattle during the evening rush, the ferry is terrible. There can be long waits for a boat and terrible traffic near the terminal. But if you can travel outside those hours it is pretty reasonable. Get up, drive on to the ferry, then take a nap, or read, or play around on your computer, or go up and have breakfast or a snack or read or enjoy the view.
If the company needs people to overlap, make a 9 to 5 shift for people living on the Seattle side and a noon to 8 shift for people on the other side, and that should provide enough overlap almost all of the time.
If a lot of people end up living across the Sound, it might even be worth considering opening a satellite office in Bremerton or Poulsbo or Silverdale. I'm not sure about Bremerton, but Silverdale and Poulsbo are full of office space that became vacant during the recession and has stayed that way. (BTW, commuting from a home in Seattle to an office across Puget Sound is fine even during rush hour, so if someone from the main office occasionally needs to work for a while in the satellite office it should not be much of a hardship).