Total rear suspension travel is total unload position, wheel off the ground to suspension fully compressed position.
The 3.5'' claimed travel is a bit unclear.
Actual measurement of the rear shock fully extended to shock snubber, integral to the shock, is 3.5" fully extended to snubber contact.
This was also confirmed compressing the shock with a hydraulic press.
Suspension to shock ratio yields an actual rear tire travel of approximately 5.25"
All of my clearances have been set to the 5.25" travel dimension.
The actual suspension travel is limited by the driveshaft to frame clearance.