Chris Perello was kind enough to answer my questions. See below.

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QUESTIONS: 
1.) (the big one) This concerns artillery on the defence.

Artillery supporting a combat may retreat (per 13.4, def. support) if the
unit they are supporting retreats or routs. Artillery alone in a hex must
stay and accept combat.

But what happens when you have an artillery unit on its fired side (it
either moved or fired already) in a hex, and the infantry unit with it is
forced to retreat? Can it retreat too, per 13.4? (But that seems to apply
only to units supporting the current combat...) Or must it stay and accept
any further incoming attacks?

To put it simply, can artillery ALWAYS retreat with an infantry or cavalry
unit that retreats, if they'd be left alone in the hex otherwise? Or can
they only do this when they were actively firing support in that combat?

2.) If you hit Panic state, can your opponent roll to seize control of
reinforcements due to enter that turn prior their actually entering the map?
(We said no...) 

3.) Line of Sight and blocking terrain. Does the terrain in the hex the unit
is in (i.e. woods) count as blocking? (Or only terrain between the firing
and target hexes?) 

Next 3 pertain to Night rules:

4.) No effect on LoS vis-a-vis spotting HMCs? Units can still see out to 6
hexes away, 8 from hills?

5.) If HMCs disrupt from moving at night, how does this affect them? If the
units in the HMC deploy while it is disrupted, are they all disrupted too?

6.) Combat: all D and A results become DR and AR. Does this apply to any
results with a D in it, or just the actual D result? i.e., would a D4 also
be treated as a DR, or just a D4?

7.) Loss of Control: if you gain control of a unit and launch it into an
attack, can you make it attack first? Or can your opponent declare the
sequence of attacks, even if a unit he's lost control of participates?

ANSWERS: 

1.) (the big one) Yes, artillery stacked with other units always retreats
with them (remember that being flipped is only a relative reduction in
combat power; the guns are still being fired, just so slowly they have no
impact on the battle.

2.) The Panic state was intended to apply only to units on the map; you are
correct. 

3.) Re LOS, consider terrain only in the intervening hexes.

4.) Nighttime LOS & HMCs. I admit, this is one that never came up. But yes,
I'd have to say they can still "see" -- the denser air at night makes sounds
carry, and the amount of noise made by a moving unit is sufficient to
indicate someone actually is there. On the other hand, a mile-and-a-half
seems excessive. How about we make a house rule now that the distances are
halved (to 3 and 4, respectively) and I'll give it further consideration.

5.) Basically, disruption never affects HMC. However, if units deploy from
an HMC during a night turn, they would be disrupted. (My Pea Ridge game
handles this a bit more neatly.)

6.) All D results become DR, A to AR.

7.) Loss of Control means Loss of Control, so the owning player should not
have a say in sequencing. Agin, this is one that never came up in
playtesting.