I have three Nikon FlexTT5's and use them with the Nikon SB-900 and SB-910 flash units along with an AC3 Zone controller. Normally I have all my flash units set in manual mode at various power settings and adjust them by taking readings from a Sekonic L-758DR light meter. I have tested these flash units in TTL mode fired directly from the top of the camera and from one of the FlexTT5's and according to the L-758DR there is no measurable difference when tested at the same exact distance. The largest variation I have seen during testing was one-tenth according to the meter, so based upon the unscientific testing I have done I do not see any issues using TTL or TTL BL on one of the FlexTT5 units.
Dodging and burning are steps to take care of mistakes God made in establishing tonal relationships. ~ Ansel Adams