Still scans folder contents if folder does not exist in the other pane's structure.

[FaceCrap]

When you compare two folders with each other and have Include subfolders checked, Winmerge is wasting CPU time by still traversing the one side existing folder and scanning/comparing the content to 'nothing'.

Winmerge should not even start to traverse a subfolder if there's no matching subfolder in the right pane structure.
Same way if it detects a subfolder existing in the right pane structure which does not exist in the left pane, Winmerge should just stop traversing right there and skip any children of that folder.
Winmerge would only need to enumerate and list files in those one-sided folders when actually opening them.

It would speed up the comparison of folder structures tremendously.

[sdottaka]

If you uncheck the Include unique subfolder contents checkbox in the Folder category of the Options window as shown below, folders that do not exist in one will not be scanned.