no advantage for me, but several disadvantages.

trunk bag will often extend over the rails, making it difficult or impossible to mount
your panniers. takes up the solid, flat space needed to carry your tent or six-pack.

if the trunk bag straps don't interfere with the panniers, you still may have to remove
the trunk bag each time you try to mount/remove the panniers.

not as versatile as bungeed-on stuff sacks.

i only use the trunk bag for local rides. h-bar bag with wallet and cell phone and
map. trunk bag has tools, spare, and pump. has foldout expando sides if i decide
to pick up some magazines or such. inside is large enough to hold a pineapple or
a couple coconuts. i never use the trunk bag for longer rides with panniers.