Dual crown stanchion position question

The answer is weight balance.  If all other things are remaining un-changed, lowering or raising the front does just what you suggest.  Lower stack, more weight on the nose, slightly steeper hta.  Generally, the handling differences you're feeling when you do this are weight balance.  It takes more or less, 10mm to equal .3 to .4 of a degree of hta (approximating this on a 62 degree hta dh bike) and that adjustment is so slight it's not doing the lion's share of the work.  In contrast, dropping the front 5mm could make a few % difference in front/rear weight balance which will be fairly profound to an expert rider.  

Regarding the distance between the crowns... that's rather irrelevant and what is important is the resulting bar height.  If you're spacing up the top crown, adding spacers below the stem that's all doing the same thing, which is raising your bar height.  Dropping your stanchions will raise the front, but will also ever so slightly change the hta and raise the bb.  

Generally, if I were using any of these mechanics to make adjustments to the handling of the bike... I would start with a 2-3mm drop of the stanchions or a 5mm spacer and do only one or the other.  I generally start with changing bar height as it's an easier adjustment to make, and it is isolating weight balance in lieu of altering weight balance as well as slight geo changes.  

First start with the manufactures reccomeneded axle to crown measurement.  This is from middle of front axle to the bottom of the frontside of your headtube(Not headset cup).

From there it's as you stated, more tubes up in clamp makes HA steeper, more grip on front wheel, lower BB, reach is longer, more twitchy at high speed, might feel too low on steep sections, might feel planted on low angle/flat trails.

Less fork tubes showing in clamps will slacken HA, less grip on front wheel, raise BB, reach becomes shorter, more stable at high sleeps but maybe harder to initiate turns, more steering flop, feels better on steeper trails.

As mentioned above, spacers between headtube and top clamp just adjust bar height and reach.  I try and balence the bike, headangle and wheel tracktion with spring rate and start at the recommended Axle to Crown, then get body position comfortable with stem spacers and bar height.  It might be hard to feel the difference at first between them, but after messing around you will get it dialed!

I would also mention its important to know most dual crowns have a minimum crown height, ie 220mm from seals to bottom of crown on Ohlins DH fork - so don't push your stanchions through too far or when you bottom out you can bottom your lower crown on the tire and suffer the consequences.

When doing any of these types of adjustments pay close attention to the fork manufactures mins and maxs for lower crown height, upper crown height, distance between the two and type of top crown to use in relation to headtube/spacer height. If Boxxer install instructions have 20 steps maybe 8 of them are dedicated to these measurements and ensuring they're within spec, which shows how important they are to follow. 

Another safe way to test is remove all the air from fork and confirm clearence from fender or tire.  For example, if I don't have a fender on, I have a few more MM to play with. With fender it could hit crown then tire at extreme bottom out.