The Clipper people can occasionally be snarky. They're more used to tourists, not business travellers or commuters, so tend to aim their rules towards tourists. I've gotten there an hour ahead as recommended and waited in the crowd forever, but have also gotten there 15 minutes before departure and got on the boat (after a couple of stern stares and harsh words from the gate person, but I got on!). The non-refundable issue is something to consider, though.
The Kenmore Air website is at www. kenmoreair.com. They're a little more expensive than I remember, but if your schedule fits for a web special, that would help.
They have a cheap special from Boeing Field (just north of SeaTac) to Port Angeles, where you could catch the Coho... oh, too complicated!