This would be a use case for composite builds, but WTP is currently not supported for composites. This will be improved within the first half of this year.
If these two projects really belong together (i.e. same repository, same release cycle), then putting them both in the same multi-project build would be the way to go.
If they should remain separate, then you can work around this problem for now by manually configuring the deployment assembly in your Gradle build to point to the project dependency instead of the binary dependency. More specifically, you can modify the final model using eclipse.wtp.component.file.whenMerged {}.