It's not uncommon to find the best combo with *no* wires matching; wire color is completely arbitrary and has virtually nothing to do with what actually goes to what, unless you happen to have a kit that all was wired up by the same person or factory, designed to be hooked up color to color.
Unfortunatley even stuff in a kit all from the same seller does not guarantee it is all going to hook up color to color, and I would guess that it is more common for it to *not* be color to color.
As for how a particular motor / contorller combo works up vs the chart, I don't know. I don't use a chart, I just use the text method posted by John in CR that's in that article. Until he posted that, I did use a 36-combo chart, but once he posted that I realized it was completely unnecessary, and almost always I find the right combo with just moving phase wires around, after I've hooked up the halls in some single order. It might take 6 tries, but it doesnt' usually take more than 3-4. The most it took was 8 (there are 8 possible combos of the three phases) to get one that worked right.
Once, that combo was in the wrong direction on a geared motor (which cna't be flipped around in the dropouts), so I also had ot use the hall switching part, but the rest of the time I just flipped the wheel around *or* used the reversing wires on teh controller. (some have that, some don't, and some reverse modes give less power than forward, so that may not be possible for everyone to do).