Simply put and a great story for the ages...As usual, this is one of those situations where WDI and Operations didn't collaborate with each other.
WDI designed it that each guest would get their own console because of how the design studio lobby, design studio itself and the show timing (3 settings) and could be up to 3 if a group wants to stay together. Problem is, no one ever told WDI about the Fastpass merge ratios. As one Imagineer said after a friend on the opening team talking to him about Fastpass ratios, "Oh god, we screwed up."
Hence, the 3 per circle was born (as well as blowing up a hole in the wall to go directly into the design studio lobby after TT became the #1 complained attraction at Epcot because FP folks were complaining that weren't getting to design). As for the empty consoles, it's because there's only a certain amount allowed in each room. The faster load is dispatching vehicles, the more you can put in a room (about 60-70). If load isn't dispatching as fast for whatever reason it may be, then the number going inside the design studio is less. So yes, you can complain all you want regarding not being to skip the design studio but it's done that way for crowd control. It's pulsing the line at the way they need it to be. If they allow everyone to skip through, it would be anarchy. If you want to skip the design studio, great, but wait until you get inside it and just walk through.