The problem is that growth is apparently everything in this game. Lower pop, means lower production and research. Or doesn't it? The game doesn't say. But It's what I would assume.
I'm in the construction-rate math right now (figuring out why it's trying to build some things it shouldn't be able to build) and I while I see a lot about tech bonuses, building bonuses, outpost bonuses, compatibility bonuses, and "how much budget did we earmark for this, anyway?" sorts of things, I don't see anything about population.
I don't know about research, but I don't think it's particularly population-bound there either. I think the general idea is that either you've got hundreds of millions (or billions) people and labor is not the constraining factor (compared to available equipment, efficiency of equipment, availability of inventive individuals, etc) and adding another billion doesn't increase said capacity, or you've only got a few million and either the game has to nerf your capacity greatly (thus consigning you to more-or-less permanent disadvantage) or just let you build/research like the other guys.
Personally I think it would be better to factor in population to some degree (never was too fond of GalCiv2's approach where population basically only produced money, not industry or whatever, iirc) but as you're pointing out here that would only hammer the Thoraxians harder. It would need to be highly scaled by the natural growth rate of said race, etc.
Anyway, I don't think the current relationship between pop and industry/research is what's hurting the Thoraxians here. If anything it's helping them.