So I know I'm resurrecting an old thread, but this is a question I've had in the past and could never get a satisfactory answer. What really confused me is that at one point I was running Royal Purple in my trans, and I got purple oil out of the transfer case when changing the passenger side CV axle.
But I've currently got the trans and transfer case out of my RAV and took the opportunity to figure this out for myself. The manual transmission and the transfer case on these most certainly are two separate units with two separate fluid reservoirs. The crazy thing is that the passenger side bearing on the transfer case is supplied with pressurized oil from the transmission via a gallery through the transfer case housing. It then drains back to the transmission via a hollow shaft. The interior of this hollow shaft is isolated from the transfer case by multiple seals. So you will see transmission oil from that passenger side bearing, but the hypoid gear is still getting transfer case oil.
The transfer case, as with any hypoid gear, needs GL-5. I'm still not sure about GL-5 in a manual with synchros, but from now on I'm going with Redline MT-90. Hope this helps.