Yep. There are no right answers when it comes to coffee (taste).
... The worry about this extra amount of water left in a siphon during the infusion is that it technically changes the ratio of brew water to grounds, and this can change the extraction. Technically. You either get a diluted optimal ratio brew, or a non-diluted non-optimal ratio brew. I've never heard of anyone who tried with-vs-without in a double-blind test, but if you find one, let us know. But this worry seems to me like an angels-on-the-head-of-a-pin type of thing. For some people it may matter a lot; but for me there are too many variables in my coffee brewing so that type of thing gets lost in the noise. I find joy instead in discovering what I like and making what I like happen. I'd encourage the OP to experiment (say with marbles and without), and see if it matters to him. If it doesn't, who cares... as long as he likes what he gets. ....
The extra water is simply dilution water - just like a bypass percent setting in a Bunn (or other) brewer when you want to make more coffee than the capacity of the brewer. Brew extraction same, with a higher brew ratio, dilute to "normal" consumption strength. It doesn't change the extraction - just the strength.
Extraction is primarily controlled by the temp, contact time, grind composition. A little bit by agitation and bloom. End strength is controlled by the brew ratio, and can be changed, significantly so, by bypass or dilution without affecting taste.
I haven't tried a DOUBLE blind, but I've presented to my wife two cups of coffee at identical strengths, same amount of coffee in identical cups - one straight and one produced stronger (higher brew ratio) and diluted by adding 45% water (6% brew ratio for undiluted, 8.75% brew ratio for the diluted) . The serving temps were within 10°F of each other (produced the straight one second, and the stronger one first - so when I diluted I used hot water to get them same temp). They were brewed with an aeropress, not a siphon, but the application is the same - siphon brewing doesn't magically make coffee that is suddenly oversensitive to dilution.
Not surprisingly, my wife could not tell the difference. She jokingly said I might be tricking her by giving her the same coffee to test her tasting ability (ahem... which I may or may not have done in the past... I don't think the statute of limitations are up on that yet ;^D)
The only time I've gotten a taste difference (and this MAY be due to changes in the extraction on a potentially erroneous assumption that a 6% and a 15% brew ratio extract the same when the same brewing parameters are applied) is with a HUGE difference in brew ratio and end strength - where the high brew ratio result is ~2 1/2 TIMES stronger than the undiluted strength brew. The diluted cup was perceived to be slightly smoother or less "bite". I thought that maybe it was a bit less bright - but we're talking pretty subtle stuff. And, it still tasted awesome.
Another explanation for hi-brew ratio/hi-strength diluted taste changes: we may have been experiencing acidic dilution (one of the suggestions I was told for people that think they are sensitive to acid - pH acidity, not the flavor "acidity"). Dilution with hot clean water should reduce the pH while diluting the coffee TDS concentration). If you have something that's brewed and is around 5 - 5.5 pH, adding almost 3X the volume with water around 7pH will raise the pH (dilute the acidity) a measurable amount, right?
Bottom line - the amount of dilution water at the bottom affecting taste - don't worry about it. It won't. All it does is change the strength - so if the strength is too weak (oh, believe me you'll know), then bump the amount of coffee (increase the coffee:water brew ratio, or reduce the mojoextract vernacular CBF, Coffee Brewing Formula or the ratio of Water:Coffee). Simple.
If you know how much dilution water is present, you can quickly calculate the expected increase in brew ratio to achieve the desired end strength - IF you have to. Most people trend to higher strengths anyway, so the amount of dilution is fairly low.
The drawdown (filtering stage) is quick compared to gravity filtered. The significant bulk of the extraction - pretty much all of it - happens during the immersion. The drawdown is akin to the press cycle on an aeropress.
(After brewing several times with a siphon brewer, I decided not to get one. I love the method, it's kool but a bit less portable than I prefer for my own brewing methods, and I couldn't justify the cost to myself).
------------------------------------------ ----------------------------------------- Le café doit être noir comme le diable, chaud comme l'enfer, pur comme un ange, et doux comme l'amour.
"There is no right answer with coffee. There is only the elixir in your cup at the moment you partake."
"...I often say that when you can measure what you are speaking about, and express it in numbers, you know something about it; but when you cannot measure it, when you cannot express it in numbers, your knowledge is of a meagre and unsatisfactory kind;..." - Lord Kelvin RECIPES thread => http://www.coffeegeek.com/forums/coffee/machines/585708
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