Having read through the links you provided: You are comparing two different things. DB’s Reisendenpünktlichkeit takes in delays caused by missed connections etc

Having read through the links you provided: You are comparing two different things. DB’s Reisendenpünktlichkeit takes in delays caused by missed connections etc. SBB’s 3 minute delay are just the individual train delays. For that DB has a similar measure which defines punctual as below 6 minutes of delay. So the difference is big (3 vs 6 minutes) but not that big (3 vs 15 minutes).