Look no further than Disneyland and their railway.
Pirates, Indiana Jones, Haunted Mansion and Splash Mountain all expand beyond the railway.
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Some go under and some go over. Disneyland have the luxury of being able to go underground which Universal doesn't because of the high water level but luckily, the HE is elevated which still gives an option to go above or below.
I love creative thinking for problems like this, it leads to some of the best experiences.
The stretching room in the Haunted Mansion exists because they needed an excuse to get the guests underground and below the railway track. It was so well received that they added it to the one in Magic Kingdom which doesn't change level.