Well, I'm no expert, but I know enough to be dangerous....
On the strut itself, where it goes down in to the knuckle, there is a welded on "tab" that ensures you don't bury the strut too far down in the knuckle; see bottom of pic, little "nub" right above the first "2" in 22-xxxx...
If you didn't push your strut down to that tab, your car would sit higher than normal. Because your perch is fixed relative to that position, it affects your ride height.
Raising your front also affects your center of gravity, and roll centers. With weight sitting higher up, it'll affect how it transfers side to side. Think of a hammer - if you hold it at the end and wave it side to side, it'll generate more force than if you hold it farther up the handle towards the head.
Roll centers, I think, and smarter guys than me will come along and advise, are kind of like a lever arm that will "push" the car side to side. Too much loading will cause the tires to work harder - but this is way over simplified, and may not be the most accurate description.
Finally, the dampers on the car control how slowly or quickly those events move the springs. Stiffer dampers cause things to "move slower", technically, I think, but the effect is events are transferred to the tires more efficiently, and they'll reach slip angle more quickly.
So, on the miata, with adjustable Koni's on it, if it's tail happy, I'll turn the fronts up to full stiff on rebound (or whatever works well...) and the front will give way sooner, balancing out the tail wagging. Same spring, right, but the damping control affects how the tires respond to controlling the spring at a different rate.
Same thing that going from OE dampers to Billy's do, or OE dampers to handling pack units.
If your dampers are "at bottom" on the knuckle, I'd think it'll settle a bit eventually, and the rest is the result of the dampers. Did you change all four corners, or just the fronts? Just the fronts would be exacerbate the effects on that end.