This setup is certainly out of the ordinary. The whole idea of enabling just one repository is to make sure that the package list are consistent with the different sections that hold the packages. muungwana has a strong point and in addition to what was already mentioned, the two repositories might not be synced at the time you might be downloading updates, hence there will be dependencies issues and broken packages. Packages in one repository might pull in dependencies from the other repository only to discover that these dependencies were not the correct ones.
In good reasons, two repositories that are not setup with the same sections enabled should be used only in special circumstances. In doing so, you are doing it at your own risk.
It should work but you are taking an unnecessary risk.