I have frequently had an issue with the linking feature because I generally would create the initial task before the document I want to reference has been put in its actual folder. IOW the file I am linking to is in an Inbox or Processing folder.
When you link a file, Omnifocus does not create an alias as that term is understood in the filing system. It just stores a string that describes the file now. You can instead embed the file, but then you have redundant storage and the problems that creates.
You cannot embed an alias file. Omnifocus will immediately get the reference to the target and embed that instead.
I have found that you can link to an alias file. So, I am considering designing a workflow in which an alias is created and placed in a special folder for use by Omnifocus. That is the file that will actually be linked. This allows me to move the original file where I like on the system and Omnifocus will still be able to find it (provided it has access to it).
Has anyone tried something like this? Any ideas?