Why are we assuming there would be nothing along those stretches? FDR Dr and 478 both run under Battery Park in NYC. The entire street could easily be enclosed in a similar tunnel with restaurants and shops along the stretch.
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We'll use the green to represent the land bridges, the red for attraction space, and the blue for shops/restaurants. With proper engineering, there is no logical reason this couldn't work, more or less. This would help ease the transition and prevent guests from feeling like they're exiting the berm into a tacked on land.
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Effectively, this is no different than having a subway tunnel beneath a skyscraper or the dozens of
bridges with buildings on them, many of which date back to the Middle Ages. The only problem is this would require a temporary closure of Disneyland Dr. with the road itself being sunken down, which would be a tremendous cost, far more than I'm sure Disney would want to spend.