Separate oil: The advantages of separating the oil, like Honda does, is that the top-end is not contaminated by clutch debris or broken teeth. Also the heat of the combustion side of the engine does not thin out the oil which is designed for your transmission and clutch. The oil in each compartment has different qualities and is designed specifically for each application.
The downside of having two smaller oil chambers is increasing the need for more frequent oil changes and even a small loss of oil can be disastrous when there is only a small supply of oil to begin with.
Shared oil: The benefits of using the same oil throughout the engine, like the RM-Z, KX-F, KTM and YZ-F, is that the large supply is less likely to run low and reach critical levels. With the larger oil supply overall engine temperatures are reduced and oil changes are not needed as often.