Because its efficiency is not only related to the module 'Salvage Ganty' that both ships have, this is what you say?
Given that both had this module plus the Shepherd had also 100 cargo I thought the Shepherd was better. Still a bit confused by the obscure optimization here.
Firstly the Salvage Rig is more efficient for its size, giving 25% bonus for 3 supply burn and 2 fuel burn, while the Shepherd gives 10% bonus for 3 supply burn and 1 fuel burn.
Secondly, Salvage Equipment hull mod has a diminishing return based on how many ships with that hull mod are present, so despite one Salvage Rig providing 2.5 times the salvage bonus of one Shepherd, it actually takes 4 Shepherds to provide the same bonus as a single Salvage Rig, by that point you have 4 Shepherds that take 4 fleet slots, burns 12 supplies and 4 fuel.
Comparison:
1x Salvage Rig+1xPhaeton+2x Colossus 25% bonus salvage,
1820 cargo capacity,
840 fuel capacity,
up to 50 survey cost reduction with hull mod,
18 supply burn,
10 fuel burn,
84 LY fuel range,
speed is 9 if you use Augmented Drive Fields
4x Shepherd25% bonus salvage,
400 Cargo Capacity,
160 fuel capacity,
20 survey cost reduction,
12 supply burn,
4 fuel burn,
40 LY fuel range,
speed is 9
For the same 4 fleet slots amd same salvage bonus, 50% more supply burn and 150% more fuel burn, Salvage Rig combo provides 355% more cargo capacity and 30 more survey cost reduction. This lets you fully salvage the occasional mining/habitat stations or ruins that gives you thousands of units of Heavy Weapons or Volturning Lobsters, or carry shittons of supplies to survey shittons of planets or carry metals to build shittons of communication satellites.
There are some factors that the comparison less straight forward, such has needing to carry 150 Heavy Equipment to be able salvage everything which further reduces the Shepherd setup's free cargo capacity, but then Shepherds have spare ordinance points to equip expanded cargo holds and expanded fuel tanks, partially offsetting this. In both cases combat ships are needed to protect the salvage fleet, as even a Shepherd with both Safety Override and Unstable injector will be unable to escape from pirate phase frigates, so neither will be able to entirely avoid combat. But you see, by mid game, the Salvage Rig would would be the superior ship for providing the salvage bonus. Once you have destroyers, Salvage Rig is greatly superior to Shepherds for most situations where you want a salvage bonus.