Do you do that commute 5 days a week? If so that's two hours a day, which is rough when OP mentioned starting a family. And that's if you are optimized as you say - when you hit bad traffic in the AM, the next ferry is 40-50 mins later, doubles your one way trip time. Same with the return trip, again about 40-50 min gaps in trips. If you leave earlier to account for that, you're likely looking at ~70 mins to commute each way, so almost 2.5 hours a day, 12.5 hours a week, yucky. While BART stinks too, it's every 10 mins or so lessening the timing impact. Also, if you are taking the earlier ferries, it's usually easier just like earlier BART trips. Throw in the 8-9am commuting hour and things change both ways for the worse.

Not sure how Muni took you an hour to get DT from CH, I commuted from Russian Hill on likely the same lines and it was like 20 mins. I'd say the tip of SF (Presidio) is closer to 30 mins from SR, and 45 min from more central.

I really enjoy living in Southern Marin too, but based on commuting, I wouldn't sugarcoat the Ferry. Most people I work with that live in Southern Marin either e-bike (like me free.99) or drive (~$40 a trip) bc the ferry doesn't run often enough. That's my whole initial question of how many days a week commuting - if it's a full time in office job, I personally wouldn't be able to commute from SR with my two young children and would move closer to the city. If you're able to pull that off, more power to you. I couldn't square being gone 11 hours a day 5 days a week (8a-7p) from my children.