Maybe they should rework habitats a bit to fill these niches. Rather than just being a population location, you can now put them in orbit of something that provides resources, and construct buildings to expand on that resource collection.
E.g. 5 mineral deposit mining station with a habitat allows you to construct mining districts that produce 6 minerals per worker (1 + the deposit value)
This would make you prize those high value deposits more as the could be magnified, but low value deposits, like 2, would only give 3 per worker, and 3 would break even.
Once they've done this, if they move habitat construction a rank or two down the tree, it might give them a good place again.