Hello Ravi,
I am not a sediment transport nor a GAIA specialist, but I would say that FINITE VOLUMES in GAIA (to solve Exner equation) can be activated when using finite elements in TELEMAC-2D (as done in a few GAIA examples like bosse-t2d, guenter, yen and hippodrome-t2d).
In the same way, I do not see why it could not be used with TELEMAC-3D to solve Exner equation but I am not a specialist as already told and have never tried with TELEMAC-3D.
My advice would be to try it.
Hope this helps,
Chi-Tuan