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I would like to modify the properties of a shortcut and set a 'start in' value.

At the moment, PlayOnLinux/Mac always starts in the .exe folder.

There is no simple way to change that, but you can edit manually Library/PlayOnLinux/shortcuts/Shortcut

The line containing cd is the "start in"
The line containing POL_Wine must be change to an absolute path if you change "cd"

Thanks!

Is there a way to add (as in windows) some text to the Target field? For example, on Windows, I might right-click on Diablo II and add -w to the target field (resulting in "Game.exe" -w in the target), to tell the application to open in a window.

Yep, configure -> shortcut argument.

Or add in at the end of "POL_Wine" line