This lets you schedule them much closer together than the conventional 3 min while still being safe.
Why? If the minimum is 3 min then it's 3 min (at least with a modern moving-block type setup). If it's safe to run them 2 min apart it's (generally) safe to run them 2 min apart the whole time.
Put another way, the 3 min normally starts ticking from the moment the train ahead completely clears the station (as in the rear of it passes the end of the platform), but in the dual-boarding setup the 3 min starts ticking from the moment the train ahead comes to a halt (as the rear of it has already passed the end of the first boarding area).
You can have one train reach the station sooner because it stops at the back of the station which is behind the front of the station, sure, and that's safe because the train is still 3 minutes behind the train in front. But that only works once. The next train has to be 3 minutes behind the train that stopped at the back of the station (and 6 minutes behind the first train), so unless you've got an infinitely long station you're not improving your overall throughput. And you have to give back the time you saved as soon as you want a train to stop at the front of the station again. Skip-stopping doesn't help, in fact if anything it makes it worse.