TL;DR: Splitters/Mergers should be shorter, so they can properly fit into stackable conveyer belt system without weird height differences.
I'll call 1 stackable conveyer belt 1 height as a unit of measurement.
If you have two lines going side by side, one height 1 another height 2, and at the same position you insert splitters, the height two split off conveyour should just go over the height 1 splitter nicely