Firstly, you're right- the project wsapi endpoint is one of the few that does not respect the standard project + scope up/down semantics that most other artifacts do.
Luckily, there's a bit of a workaround, in that you can use the special {projectOid} token in queries in the custom list app to create something like this:
((Parent.ObjectID = {projectOid}) OR (Parent.Parent.ObjectID = {projectOid}))
You'd need to add some more Parent.Parent.Parent clauses depending how deep your hierarchy is. This is not a perfect solution by any means, but it might help a little bit?
The full list of supported tokens for custom list queries is here in the help: Build App Queries | CA Agile Central Help