The extra 3.5" from link pivot to axle center-line is a messy measurement as the axle housing is relatively horizontal throughout movement and only the links are rotating creating travel. If you had a radius arm then yes the axle would swing down and create more travel. With a four link the swing is minimal and should not add measurable travel. I pulled the numbers I had for yours from a cad sketch showing the trialing arm swing from horizontal and shock travel from mounting eyes. The difference is 1-7/16" travel between a 36" link and a 39.5" link. The most accurate way is to measure the shaft travel and the trailing arm pivot point travel in relation to the frame. Big picture is up travel is more important than down travel and excessive down travel might be limited due to drive-line angles or mess with the spring preload and downforce to the point that it is not worth the excess droop.I used the information HERE to determine my rear wheel travel numbers.
Wheel travel = Shock travel x B / A
Shock travel = Wheel travel x A / B
A = B x Shock Travel / Wheel travel
One thing to keep in mind, the 36.00" dimension is only referencing the trailing arm, not the whole suspension system. In reality, that dimension is ~39.5". The rear trailing arm bolt is 3.5" from the axle centerline with the Goat Built lower control arm mounts.
Wheel travel = *C/O Shock travel (12") x B (39.5") / A (23.5")
20.17" of travel (not currently using 100% of c/o travel)
Wheel travel = *Bypass Shock travel (12") x B (39.5") / A (28.5")
16.63" of travel at bypass limits (this is the limiting factor)
I am getting the full 16.63" of travel at the wheel, using all the travel the bypass will allow. I am adding limit straps, and already have the bumps installed to bottom out at the same time as the bypass shock.