So with drop spindles, the car sits 2" lower before you contact the bump stop. Or, if you think of it another way, the k-member, pan and headers are 2" closer to smashing into the road before you contact the bump stop.
There are lower profile bump stop pads out there, or you can cut the rib off the center of a factory pad. Either way you trade a little of the progressive nature of the factory pad for more clearance.
Yup. The drop spindle moves the wheel axis up 2", so it lowers the car 2" without changing the torsion bar adjustment. But it does add some bump steer, and it does raise the roll center. Not a huge problem, you're still probably ahead of the handling game vs stock because of the lower center of gravity, but at least in my experience I can get as low as I want to be without using the drop spindles.
Here's the thing with the factory bump stops. They were in fact designed to act in a progressive nature, adding rate as the car neared the end of its suspension travel.
BUT, with 100-120 lb/in rates you NEED that progressive bump stop feature, because otherwise you'd constantly be slamming the suspension into the frame. With a 1" bar, your spring rate is ~200 lb/in depending on the manufacturer, so you don't need that additional rate. And the shock technology out there today makes it possible to have that high of a rate and still have a comfortable ride, which is something the old shocks couldn't do. Hence the smaller torsion bars and giant rubber bump stops.
With 1" or larger bars, you don't have nearly the amount of travel to worry about, and you can use the smaller bump stop as long as you've set the ride height up so that you're not going to be constantly hitting it. If you do that correctly, you shouldn't hit the bump stomps at all during "normal" driving, and you'll have a nice, constant, predictable spring rate to count on.
The stock bump stops certainly give you a larger margin for error when setting up the suspension. But the factory was setting up tens of thousands of cars, you're only setting up one. And they couldn't get a set of Bilsteins to make a 1.12" bar ride well, so they undersprung the suspension and added progressive bump stops. Even with 1" bars you should be able to lower the car significantly without worrying about ever hitting the bump stops.