The scout pet is generally worse damage, especially solo.
I say generally because like you, in certain circumstances I can show zonewide parses that are pretty much absolutely identical comparing scout and mage pet. In a group built around melee dps and especially with no Troubador, and very few multi-enemy fights, I've found the damage to be very similar. Soulburns are ~20% more damage which can make up for the lesser dps of the scout pet.
But.. in most scenarios, you're probably best off with the mage pet since 'the scout pet can put out about equivalent damage' is not exactly a stirring call to arms to bust it out.