I honestly think the devs just didn't like the idea of people spamming habitats everywhere. I tend to feel the exact opposite. At some point there should be downsides to making infinity habitats, (or just better tools for mass spamming them) but voidborne civilization is basically the future. Engineering wise its the best way to go, what with the huge amounts of easily accessed shit floating in space, and the relative low mass cost of habitats once you have strong enough materials to make them. I think the game should embrace the goodness of habitats instead of rejecting them. The game should have distinct phases. The planetbound phase of small fleets and terraforming, the voidbourne phase where you learn to harness the resources of the void and gain access to an order of magnitude more resources and power, and then a phase of darkness as the galaxy is devoured by dyson spheres, mass synthesizers, and massive fleets beyond the comprehension of us mere mortals.
I personally dont think there should be any real regard for allowing very low tech empires to compete directly in any meaningful way with later stage empires, and that aspect of truly asymmetric survival (if it ever even happens in MP) is a very sci-fi concept and potentially pretty fun if you can find various political and cultural ways to convince your far more advanced peers to leave you alone.
Heck, it would be cool as hell if the galaxy map slowly went black to reflect the dyson spheres eating everything.