Hutch
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But will the yeast S-04 be able to carbonate the bottles after all this time if it flocculates so well? Won't it all be dead/in the yeast cake by then if it takes 3 weeks from pitching to bottling?
Don't worry about the yeast after 3 weeks. Yeast will survive many months/years once it's settled-out in beer. It does eventually "autolyse" (die) at the bottom of the fermenter, but in this short time-frame there is nothing to worry about.
Many experienced brewers do not use secondary fermenters, prefering to leave the beer in primary for extended conditioning after it has reached final gravity. The primary reason is to avoid unnecessary exposure to oxygen by transfering to secondary. There is a perceived risk of fouling the beer by leaving it on the yeast cake for longer (due to autolysis), however a few weeks is not going to do any harm, and basically avoids extra work in cleaning/sanitising a secondary vessel and racking tube.
Transfering to secondary is useful if you need to free up your primary fermenter, re-use the yeast cake, or you wish to dry-hop in secondary.
Do what works for you.
Hutch.