Here's the reply from Olympus tech support (kudos to them for replying within a few hours):
It is not possible to use the setup you describe using the wireless flash control setup in the E-3. The built-in flash must be raised, since it is the wireless flash controller. An on-camera FL-50R is not possible because it can't be mounted in the flash shoe when the built-in flash is raised, and putting the FL-50R on a bracket mounted on the camera because the FL-50R would be outside of the line of site needed for wireless flash control.
If you use a flash by connecting it to the PC sync port on the E-3, that flash will not have TTL functionality. Further, if the flash connected to the PC sync port is a thyristor flash, the exposure would have yet another factor to confuse the TTL metering of the wirelessly controlled flashes.
Cheers,
Andreas