Skim 1.5.5 (121) on OSX 10.14.6 (18G2022)
The order of open, tabbed documents is shuffled when a new document is added.
Example:
I have 4 documents open in tabs. They are laid out left to right in a particular order for my workflow.
I open a new document.
Windows > Merge All Windows causes the carefully organized documents to shuffle around. The new document is always on the far left and in focus.
This is unnecessary and disruptive.
That feature is implemented by Apple, we have no influence over how it
works.