As far as I know the linked brakes are activated with BOTH levers, front to rear and rear to front. I don't know if there's a sort of modulation going on depending on which riding mode you're in.
As to your question, you're spot on, I come from a big (1000cc) japanese inline-four which barely has any engine braking. I had a Multistrada for a few months and I had to get used to the engine braking as I normally would let off the throttle earlier and correct the entry speed with the brakes. On the Ducati the linked brakes were only activated with the the hand lever for the front brakes and in "Sport" mode, the linked brake system was deactivated so you could use the front and rear brakes independently.
