There are two completely separate questions here:
A. Can I use a single qubesctl call in this case?
No. It’s hard coded in to qubesctl that it will handle states in this
order - dom0, Templates, qubes.
You have to use separate qubesctl calls in this sort of case.
B. Can I make salt state on target A require a state on target B?
This is more difficult in Qubes because we have no master - ordinarily
you would use orchestration or runners to make this happen.
What you can do is make state in A depend on the result of state in
B - you can do this using jinja, by checking the outcome of
the state (e.g. does B have specific feature set?), or by writing pillar
data on completion of state in B, and checking that data in state on A.
There are probably other approaches too, but these are very easy to
implement and work well (for me).
As always, a concrete example would help.
I never presume to speak for the Qubes team. When I comment in the Forum or in the mailing lists I speak for myself.