Considering I understood correctly, the message shown in the graph editor is a known GUI-only bug that exists because of the variable previewing the overridden value. The GUI inspector code “sees” a Unity Object being referenced in an asset and as such shows that message, which is a false positive since things will still work fine in runtime after all (please confirm that this is indeed the case for you too).
I have “fixed” that by basically removing the exposed variables override value from being previewed in the next version unfortunately , since that was creating a lot of confusion. The one you mentioned being one of them and another confusion being when editing multiple GraphOwner prefab instances using the same Asset Graph but having different exposed variable overrides (there is a GUI-only bug there as well).
Thank you.
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