There is a way to define a per-project prefix for each function/global vairable/typedef that coder generates. But you have to have Embedded Coder license to get that feature. If you have one, then in the settings (more settings / code appearance / identifier format) you can add a custom prefix to all of the identifier types.
The other problem that you mentioned (file named rt_nonfinite.cpp that is in both projects) has no proper solution. But the file seems to be identical in between the projects, so I think you can just overwrite it when copying files from the 2nd project to the common folder.