When merging between inputs that have layers in different orders, the merge happens with the layers in the original order and then the layers are reordered at the end. This can cause unintended results.

While this can be worked around, by creating visually identical layouts containing layers in different orders, I think adding a "Merge2" transition that performed the reordering first would be a more efficient (operationally and computationally) solution to a lot of cases.

Example.
You have a number of picture in picture layouts you wish to transition between

Input 1: background
2: slides
3: presenter
4: layer order 1 2 3
5: layer order 1 2 3
6: layer order 1 3 2

Merging from 4 to 5 works fine with green expanding while blue moves across, it also works in reverse.
But merging from 4 to 6 results in blue expanding to fill the screen and then green appearing in place. It works ok in reverse.
An alternative merge transition that did the layer reordering first would make a smooth transition from 4 to 6 possible.

Creating a duplicate of input 4 and reordering the inputs, then cutting to that before merging is a solution but with more layers the number of versions needed grows quickly. A "Merge2" should avoid the need for many of those.

Thank you. I've given that a go and can see it working well in this example.
I still feel the option of a merge with the layer reorder at the start would help keep things clearer