1) Yes, you might find that running an A/A test on your data shows a "result" for one of your groups, even though there obviously is none; this (as I see it) is just due to insufficient data. Isn't running an A/A test isomorphic (in a strong sense) to correctly checking the statistical significance of your A/B test, and only believing your A/B test if it does in fact reach a high significance threshold?
2) Re-randomizing your data the way they describe will inherently increase the "orderedness" (decrease the entropy) of you data set, which risks biasing the A and B groups in some what you don't fully understand. It seems like the re-randomization procedure would at best leave the statistical properties of your A and B groups unaltered, and at worst introduce a new bias that makes your result fishy.
I'm sure there's something deeper going on here, but the post doesn't explain it well.