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As you mentioned, this setup should theoretically work as the secondary drive would be the one paired with the Intel® Optane™ Memory and they two would be linked to the Windows* partition in your primary drive, which means the Ubuntu* partition would be invisible for them. However, I cannot tell you if this setup will indeed work as this configuration is not validated or tested. Actually, this is a not supported configuration and the results are unknown.
Having said this, you can still try it, but it’s up to you as we don’t recommend to set the Intel® Optane™ Memory in this environment.
Have a nice day.