Under what circumstances can aluminum be in contact with steel?
Unfortunately, you're correct:  the moisture in the air can and will affect both.

In reality, both of the scenarious you describe happen pretty often.  Sometimes it's terrible, sometimes not.

The ultimate choice for you is a balancing act based on practicality:  How easy/cheap to install vs. how meaningful/terrible are the consequences (and after how much time).

When it comes to flashing, I'd do it right, first time, no exceptions.  The consequences are just too dire for a poorly done job.

As for using an aluminum patch on a gavanized duct:  yes it'll corrode after a while.  But no big deal IMHO.