Did another inspection this morning and came across this. Occurs both of the left and right side.
If you can't really see, the steering knuckle is hitting the lower control arm.
If it helps, during the install there was a lot of issue getting the strut to fit its way in, so much that the shop had to lower the crossmember, place the strut in, hook up the control arm, and jack up the crossmember.
EDIT: Called Zone and apparently the digging into the stock LCA is normal. Still unsure about the clunking, the tech suggested considering a rear driveshaft spacer or lowering the bilsteins to stock height.