Will silicone caulk seals affect the bond of mortar and tiles to backer board?
Your silicone seals should never be wider than about 1/2", and you should avoid smearing caulk onto the face of the backer board. Your mortar and tile will span those small gaps without an issue. Keep in mind that the boards should all be securely fastened to the framing such that there's no movement with respect to each other.