They still do use the physical queue though. When your boarding group is called, you still have some waiting to do, just not as much. A decent chunk of the queue has been used all this time, regardless. More than likely a physical only queue will spill out onto the pathways, at least for a bit.
Not to mention, when they're doing boarding groups, people just go wait in other queues, see a show, eat lunch, or leave entirely if they don't get a group - especially after the afternoon groups fill up. It's kind of amazing how many people walk out after they fill up for the day. Some leave completely while others work their way to another park, which pretty conveniently, park hopping starts at 2pm.
When there's a physical queue, that exodus won't happen - at least not to the same extent, making the crowd more lasting. The park will be busier at night, I believe. Which Disney would probably like. As long as there's a chance, some people will stick around for it, instead of park hopping. Something that might even happen is for more people to park hop to DHS after 2pm, which has been a bit more rare lately.