Well.... not quite. While Scooby Doo (the coaster, aka Beastie, aka Fairly Odd Coaster, aka Woodstock Express) can be seen in the background, Mrs. Brady is not standing in Hanna-Barabera Land. She's standing in a behind the scenes area, specifically right in front of the Administration Building. That building is also where they shot the boardroom scene, in which Mike pulls the Yogi poster from the tube.
What I find interesting (along with the running scenes that you pointed out make no sense if you know the layout of the park), is that when they're running through the park, it's sunny, but when they're in front of Admin handing the plans over to the executives, it's raining. You can't really tell by looking at the actors, but the ground is wet, you can see some raindrops to the sides of the frame, and there are a few rather large raindrops that pass right in front of the camera lens.
I love that I have this episode (ok, ok, I admit... I have all 5 seasons!) on DVD, and The Partridge Family episode on VHS so I can watch them anytime I want.