This is rather older, but here's a post from Nikita Popov explaining the difference in storage in PHP 5.4:
The structs have changed dramatically in PHP 7, but the basic optimization he describes is still with us, and is the reason for these results.
Some more recent posts on the topic, too:
https://nikic.github.io/2011/12/12/How-big-are-PHP-arrays-really-Hint-BIG.html
https://nikic.github.io/2014/12/22/PHPs-new-hashtable-implementation.html