I wouldn't one-box at 1:1.01 odds; the rule I was working off was: "Precommit to one-boxing when box B is stated to contain at least as much money as box A," and I was about to launch into this big justification on how even if Omega was observed to have 99+% accuracy, rather than being a perfect predictor, it'll fail at predicting a complicated theory before it fails at predicting a simple one...

...and that's when I realized that "Precommit to one-boxing when box B is stated to contain more money than box A," is just as simple a rule that lets me two-box at 1:1 and one-box when it will earn me more.

TL;DR - your point is well taken.