Thanks for the reply! It’s partly because the migration is not yet completed, but also - working with workspaces is not a must, many times having project with different targets and dependencies on other projects is sufficient.
So the setup is quite simple - a project which is simple enough to be a project and not a workspace, and it depends on another project, generated with Tuist. One can always change the structure of the projects that depends on the Tuist-generated one, but I would expect it to not be dependent on using workspaces.
For my case, using the workaround mentioned above was sufficient, but maybe it can help someone in the future.