The rules that you were given apply after the completion of the group games. These rules are taken from UEFA. A quick google turns up the "Regulations of the UEFA Champions League 2012-2015 Cycle Document Season 2012/2013" - there might be other more recent ones I don't know. The fact that they state they apply after a group is completed is enough to make me think that classification could be done differently prior to completion.
On the other thread I gave you my best guess on that pre-completion classification but I don't know - doesn't affect the outcome. I'd further guess that the table positions are different because sometimes head to heads are completed, sometimes not but I'm just typing in white space because I don't know.
I tried to help by applying the rules to your position to help you understand why you are out of the CL. Hopefully you understand now that Pasta Boys go through because they scored 2 away goals against your 0 away goals.
If you want to investigate if there are any differences in how tables are shown prior to completion of the group games then you are welcome to do so, unless someone else knows.