Launching at Anacortes gives you an easier run to the San Juans - less open water to cross. I don't know the facilities - whether you can launch & leave a trailer/truck at Skyline or if you have to go to Cap Sante. Someone else would know...
Launching at Port Townsend means crossing the Straight of Juan DeFuca. Can be a fun crossing. You'll need to watch currents carefully when you enter Cattle Pass (between San Juan and Lopez Islands)
Also, getting to Port Townsend could be as challenge - I don't know when the Hood Canal Bridge is opening, so the only way to the Olympic Penisula is by going west at Olympia.
When is Day 1?
Mac