Hello,
I made a similar model that checks to see what FCs in a geodatabase have a GlobalID field, and which ones don't. Then the model adds a GlobalID fields to the FCs that don't.
If a precondition is false, and that tool in the model doesn't run, the messages usually reflect that.
So I see the same warning when my model runs through successfully.
From what I am reading you aren't having and problems with the results of your tool, correct?
Adam