I have experienced that the jhbuild step put it's stuff into WebKitBuild and does not consider WEBKITOUTPUTDIR. Don't you think it should be fixed? I don't know much about this tool and the Gtk build, so I would ask for a fix here.
Is this a duplicate of https://bugs.webkit.org/show_bug.cgi?id=76161. For some reason I don't see this problem.
*** This bug has been marked as a duplicate of bug 76161 ***