As an E-PL3 owner, I thought I will give it a try. I modified one of my two strobes, and indeed got a much weaker light. To test the effects on TTL, I did a semi controlled test (see attached pictures). My conclusion is that there is little difference between the two strobes when using an external strobe in TLL mode. The differences are mainly at the extereme ranges of apartures.
E-PL3, Olympus 60mm lens, T 1/160 throughout.
External strobe YS-D1, set on TTL with the TTL dial on 0. The strobe was on the right of the camera facing so that the edge of the beam was on the object. The strobe was connected with fiber optic cable. I was holding the other end of the cable about 2cm in front of the camera strobe. I checked that the hand blocked any light from that strobe (you can also see that from the shades in the images).
I varied the strobe setting of the camera and aperture, as noted in the attached picture. I converted the images from raw to jpeg without any adjustments.
My conclusion is that the camera changes output by modifying duration of the flash. The modified strobe had slightly lower exposures throughout the test.