Hi,
We are facing some Graphviz/Dot limitation here.
You can use the "left to right direction" feature:
@startuml
left to right direction
[A]
[B]
[C]
[D]
[E]
[F]
A-->D
B-->D
C-->D
D-->E
D-->F
@enduml
I don't know if this is a possible solution for you