On my FXDL 2nd from the bottom for my 200lb.

 

Changing the tension on a single-rate spring can't cause an increase in stiffness, because it's single-rate. If your spring is 50 lb./in, that's 50 lbs. in the first inch, but also 50 lbs. in the fourth inch. That means it takes the same amount of force to compress it by one inch regardless of how many inches it's already been compressed.

Did you observe the length of the shock while the bike was fully loaded while adjusting preload, or while it was sitting unloaded? A more accurate measurement than the length of the shock is the amount of sag, as it's a larger measurement and any changes will be more obvious and easy to measure.

Edit: I should mention that there are setups where suspension geometry is such that there is an increase in stiffness even with a single-rate spring, generally found on some sportbikes, but the Dyna is not one of them.

 

Adjusting my shocks never changed the height, but rather increased load capacity. This seems to be realized by a better ride and the fact that the bike will not seem to 'hit' when you encounter bad roads. But these facts seem to differ based on lots of things. Actual shocks, weight, ride desired, road condition....etc

Anyway, whatever setting you are using when riding 1 up should be increased slightly when extra weight is added to the bike. Keep track of incremental changes and the results so you can adjust as needed progressively.

 

Here's a good article about it:
http://www.sportrider.com/tech/146_9510_tech/index.html

A properly-designed rear suspension should be within 0 to 1/5 of an inch of topping out when the bike is unloaded. This would be why there appears to be no difference in height when increasing rear preload. The difference in ride height can only be observed while the bike is loaded. So with one or two people aboard, with their feet all on the pegs, and with someone else holding the bike to keep it from tipping over, and someone else measuring.

Obviously this is a PITA, which is why Harley included preload setting recommendations in the manual.

 

Without over-complicating the situation (which is easy to do when talking about suspension), the bottom line to the OP's question is "Yes". You should change the shock setting based on the load...

 

Well I will admit you submit a facet that I have never really honed in on. I read the article in the link. So basically by pre-tensioning the springs (cranking up the shock) the springs stiffness is not increased (granted) but if I read the article correctly it's compression window is decreased. Thereby making the compression rate occur faster and in a short distance of travel as opposed to the non pre-tensioned shock.
So then you are referring to ride height with the passengers on. Yes I agree with that. I thought you meant that it changed the height of the bike just by adjusting the shock. So there is no disagreement from me there. I just never really thought of it expressed that way. But again adjusting the shock does not change the length of the shock. I agree that it will cause the compression travel distance to decrease as the shock spring reaches it's compression limit in less distance. But to me this is kinda overcomplicating the viewpoint. Even though technically I admit that the springs stiffness does not change, by decreasing it's available compression travel distance it's about the same effect.
Always ready to expand my perception though.

 

Two up, I ride with mine set right in the middle (3). Seems to feel the most comfortable for the two of us and doesn't bottom out like it use to unless I hit a pretty nasty bump.