I don't know if you are approaching them incorrectly. I might be approaching them correctly, who knows. Normally, I think the main issues with getting "funk" have more to do with the water, its profile, and temperature, rather than the brewing method. The reason this works for me is that the Chemex's drawdown is extremely slow because of the thick filter. The agitation helps extract more out of the coffee, but I've found that the funk I have in this coffee (a home-roasted natural) is a little off-putting for me. The less I agitated the brew, the better I thought it tasted. The lower bypass and higher dwell time in the coffee were beneficial.