This is my guess - it's hard to know without seeing the whole pattern or a picture of the bag (is there an online link?) - The only way to do K2tog without messing up the K2P2 ribbing would be to knit the two knits together. That might sound like a no brainer but I find their instructions rather confusing where it says to "....make eyelet holes on every alt knit st by k2tog..." I think perhaps it means to do the eyelet holes on every alt (every other) set of knit stitches in the rib? So this is how I'm picturing it - and I could be wrong, but....
(K2tog, yo, P2, K2, P2) repeated to end
So every other set of knit stitches in the established rib pattern would have an eyelet.
Then when it says to do another 3 rows in rib pattern, yes you would go back to doing a regular K2P2 across. The eyelets are just for that one row.