What is the set of things that differentiate one application from another from the point of view of right-click on dock icon -> Options -> Assign To (All Desktops / This Desktop / None)?
I've experimented and haven't been able to hit on a combination of actual binary name / Info.plist values / PkgInfo string that will make Mac OS X workspaces think a duplicated application is different from the original for purposes of automatic desktop assignment.
Best Answer
Found it, just leaving this here to make it easier for others to find answers via google. See:
Assign Application Windows to Different Spaces/Desktops
Is there a way to hide certain apps from the cmd+tab menu?
Specifically, the one thing you need to care about is CFBundleIdentifier in the app's Contents/Info.plist file. Here is a part from a script that may be useful:
To see this in some context, see my answer to this question: Is there a simple way to have separate dock icons for different Chrome Profiles?