Here is the review by Tundra Headquarters of the Truxx 3" lift.
Truxxx Tundra 3" Lift Kit Review | tundraheadquarters.com
It is spacer above the strut, making it longer. The review addresses the concerns you have. Bottom line, jury is still out on that one (whether or not it causes harm). They prefer the Toytech, which is a coil spacer. Toytech and Tuff Country both make a 2" front only coil spacer. It leaves the truck with a little rake to it for towing/hauling.
Myself, I think I am having the Tuff Country 2" put in. It's a temporary solution until some of the other manufacturers come up with some reasonable coil/shock combos that don't break the bank.