First of all, we’re more or less on the same boat. I mean, I still prefer thralls over pets, but I agree with you that the power difference is just ridiculous, and pets sharing population limit with thralls makes them even less appealing. I don’t even want them for decoration purposes for that very reason.
That said, given the amount of stats you can get via perks and leveling, armor is more often used as a tool to offset bad RNG than to buff a particularly good thrall (which, of course, happens too). The max amount of strength you can add via “mass produced”, easily-accessible armor is a meager +9, though. To add the +3 of the warpaint you need to use dragonpowder, and they last longer than on players, but still wear off afaik. To get a +3 helm to replace the +2, you need to farm a particular legendary. Same goes with the chest, which also has the trade-off of being light armor, which deprives the thrall of the highest armor piece in their equipment, or to craft Redeemed Legion chests, which are “mass produced” too, but need a Purge Armorer to be crafted. The +3 gauntlets require (after T4 armorer reductions) 14 armor scraps, farmed at Warmaker’s Sanctuary (which would net you about enough to make one of those every 15 minutes) and another dragonpowder. All this combined nets you a +16 STR bonus, and to gear just one thrall up to this point requires a lot of time and effort in farming materials and grinding bosses and/or being very lucky with purges. I guarantee you, most people won’t go these lengths to squeeze a few more strength/vitality points.
Bottom line: it’s not that thralls, by virtue of being harder to find, knock, gather and break, are somewhat stronger and more durable than pets as-is, and are also given the access to enormously buffing armors. It’s that, being somewhat stronger, they are also given access to a system that can potentially further improve an already lucky thrall or at least make a little more viable an unlucky one.
I agree with you, though, that pets could (and should) be buffed. Special meals that buffed them, warpaint-style, would be a good first approach, though. Allowing you to be escorted by both a pet and a thrall would be great, too, and would give us a reason to actually try to breed and raise good pets. Giving them their own population limit would be even better, too! Pet armor would be freaking awesome; but, given the amount of different pet types in the game, it would take a lot of time before we saw any of that. Maybe just sized armor? Like, giving the small armor to wolves, tigers, hyenas, etcetera, mediom-sized armor for bears and kappas, and big armor for rhinos and elephants? Spiders, scorpions and sandreapers would need their own armor category, but for the sake of simplicty I’d be willing to throw away realism and allow them to share one armor type. Skeletons and ghouls can use human armor, after all.
On a little off-topic side note: sandreaper queen is overrated. Too big to fit through doors, so she can only be effectively used outdoors since she can be killed from outside the room she’s in. Her poison stream attack isn’t a threat if you pack a lot of antidotes or, even better, spec for the survival perk that renders you immune. A pet or thrall with relatively high survival will receive just a few ticks of poison and then it’ll just wear off. Nah, mate, hear me out: Silent Legion warrior. Created through necromancy, requires one fragment of power and six hours (but since it’s created in an alchemy cauldron, it can be greatly reduced). It only has a 15% chance of spawning as a result of necromancy, but it’s worth it. Hits like a truck (by pet standards, at least), good HP pool, immune to bleeds and poison/gas, and applies corruption to players hit. Plus, it’s human-sized and, if it ever gets killed (again), you can loot a free Telith’s Lament from its (re-deceased) corpse.