The bind variables you talk about are Global to the App. We happen to code access to them in the project manager but they really have nothing to do with the project manager.
When I define a var and value pair in the global bind vars I do not get prompted when used in a SQL statement in SQL editor or Query Builder.
Global bind vars seemed like a good idea at the time. What is your use case? We have some other bind variable support in publishing to Toad Intelligence Central that provides more shareable value.