For the commander rule I thought about something that might be useful... as house rule of course.
What does a commander do? Leads troops. So yeah there needs to be something that reflect this. Actually the combined engage is a specific leading; coordinating two or more formations as a whole. As most stated, this may not be enough, since you don't always want to;
-combine formations (losing activations rapidly)
-engage at all
Here we go. There needs to be something general, which is good for all kind formations and units, not breaks the rules / balance etc.
I go back for the very basics; activation. Whenever a formation fails it's activation it takes a Blast Marker, and can only resolve a Hold action.
So how about a formation lead by a commander, failing an activation test, NOT receiving a Blast Marker, though still restricted to Hold action?
For me the failed activation is a situation where the HQ orders are not received properly / at all and thus the formation gets disoriented, confused or idle. This time a commander steps in with his authority (especially if he is the supreme commander himself) and issues small scale, not preplanned order. (which is the Hold action)