The first thing that comes to mind when I see these indexes is to understand how the index was built and how the collection lived so far.
When an index is freshly built (as it’s _id in this case, when the collection was created) it’s very compact and optimized. But as docs are added, removed, added, removed and updated, the entries start to spread and keep space in between.
If you rebuild an index it will be very compact but also have no space in it, if you then add things to it that are spread through the index it can rapidly grow as it has to split every block to make room for new entries.
So depending if the collection are freshly loaded or used for years, this can make a huge difference. It doesn’t mean that this makes the index less efficient though. Performance issue could be related to a bunch or other reasons.