The spring looks like it's correct on the perch. It appears like the rubber mount at the top should be turned a slight amount so that the head of the bolt fits into the recessed area of the rubber isolator. That's the way I see it from your pictures.
I'll have to take a look but I swear both the OEM and the replacement Tacoma springs I installed had that spring top ground down just a bit. Your photos look like they cut it with an axe. The end is kind of mushroomed...eeek..