First that is not how TTL works. All that happens is that when the camera flash turns on the external strobes turn on and then the camera strobe turns off the external strobes turn off. One strobe would not stay on longer or burn brighter because of a stroger light from the camera strobe. If you set the camera strobe to manual at say 1/4 power and both external strobes go off then they should both TTL when set to TTL. All the camera strobe is doing is turning the external strobes on and off. It does not matter if you use full power or 1/64th power the strobes will still put out the ammount of light they are set for in manual and the same is true for TTL.
Phil Rudin
Not what I'm saying ....
For example, in manual mode at 1/4, the 2nd (rightmost strobe/innermost fiber optic port) will FAIL to fire sometimes (frequently).
In wireless E-TTL mode, it may fail to fire the rightmost strobe entirely, or fail to fire the pre-flash, or the subsequent calculated flash. It would appear that sometimes, in E-TTL, the 2 pre-flashes are correct, the calculation is performed based on both pre-flashes, but only the left strobe is then fired (and at roughly half of the calculated value). Of course this all happens so fast it's not possible to visibly confirm the pre-flash/"real" flash sequence.
Both of my UFL-2's exhibit the same symptom when swapped. Both of my strobes are on the same channel and group.
You may have oversimplified wireless E-TTL on digital cameras .... the UFL-2 strobes and the E-PL1 in wireless E-TTL mode mimic the popup strobe operation and requires the pre-flash to calculate the strobe intensity. From Olympus: "The flash group, channel and settings are then set up on the flash units. When the camera shutter is tripped, the cameras built-in flash emits a very high-speed burst of data in a pre-flash that commands the performance of the flash units". What you described for TTL is similar to how TTL works on film cameras or how Auto mode works on most strobes (at-the-strobe sensing instead of camera body sensing). I'm not sure of the exact E-TTL methodology for Olympus but I am familiar with Canon and Nikon .... I believe Olympus is similar enough.
In the below pics, the center-to-center of the ports is 15mm. The outside-edge of clear portion port 1 to outside-edge of clear portion port 2 is 21mm. The length of the flashtube lens is 16mm. The actual flashtube is 14mm.
Please note that even if the alignment were perfect, the flashtube is only 14mm long and the outside-to-outside of the ports are 21mm. In order to get the flashtube to cover both ports, the ports would need to be about 10mm center-to-center ... or .... the flashtube would need to be about 21mm long.
It looks like the designers didn't account for the width of the 2 black sides next to the flashtube on the popup.
The alignment (as shown) is off center and the innermost port is about 90% covered by the popup cover.
Conversely, as shown in the last 2 pictures, the E-520 housing has ports that are center-to-center 10mm and the flashtube is 19mm long. Or, to put it another way, both of the ports are within the width of the E-520 flashtube (and the alignment is correct .... no offset). You can actually see that the gap between ports is wider on the E-PL1 housing than on the E-520 housing.