Taxation Law Conundrum - Section 68 vs. Rule 11U

I mean, seriously, is it just me or is Section 68 of the Income Tax Act, 1961 totally confusing? We're told it deals with 'deemed income' when a business receives cash without a valid transaction... Okay, got it. But then comes Rule 11U, which seems to contradict the very purpose of Section 68. It just states that if an assessee can't provide a PAN to a bank, the entire transaction is invalid! Can someone explain to me how Section 68 applies in such a scenario? We learned that even a single instance can trigger the entire provision... But wait, doesn't Rule 11U just throw it all out the window? Anyone else as lost as I am?