4 star rank 3 relic (Thor) does more damage than a 5 star rank 3 relic (Gamora)

mvnceable

GalactikDonut

thors just him

Wong_98

The star rating of the relic didn’t enhance the damage the relic does, it only enhances the relics abilities. The relic’s damage comes from your champs current attack

Magrailothos

It looks like with Thor, your Aptitude buff came before the Precision/Cruelty buffs.

With Gamora, the Aptitude buff is the most recent; so presumably didn't enhance the Cruelty.

So I think that the difference is due to the Cruelty Potency.