I have a feeling you are absolutely correct concerning different perch location.
I happen to have a friend’s TRD Pro Tacoma kit PTR13-39150 (same 6112/5160) sitting in my garage....was able to measure center lower shock eye to perch......9 7/8”. I believe the Tacoma kit coils are 600lb 14”. This Tacoma kit is assembled with top hats and the pre-loaded mounted coils measured 11 7/8”. Seems like a lot more pre-load on these Tacoma coils compared to the FJ kit coils. Also, I wonder if there is a lot of difference between the extended shock length of the Tacoma vs FJ vs T4R Pro kits. Look at this link as well. Some of the Tacoma kits were mistakenly shipped with T4r Pro coils mounted which are shorter coils....see link below post #2652 and read on.
https://www.tacomaworld.com/threads/ptr13-35150-bilstein-trd-pro-kit-upgrade.530072/page-133
This makes me think that the Tacoma Pro kit and T4r Pro kit 6112s might have similar perch locations...and this FJ kit 6112 perch location is lower (less pre-load) compared to the other two.
*Definitely need a T4r Pro 6112 perch measurement.