I don't want to remove or reduce the penalty (with default settings). Rather, I will try to find some way to make domed cities more useful on mature colonies. Again, my goal is avoid boring gameplay by forcing the player to consider the positives and negatives of different terraforming options instead of just duplicating an "optimal" configuration on every planet.
in that case i'd definitely recommend things such as an accessibility boost. Or partial reduction to thermal hazards. perhaps special bonuses for commerce when the dome is present. or any number of other upsides that could potentially make it remotely worth it when playing with nexelerin.
i do personally agree with basileus. unless you have managed to be super friends with everyone in the sector till the end of time. no matter how much you want to use them, they are just not an option unless you for some reason colonize an awful world where you HAVE to use dome to eek out a working colony. and by the time you reach a point where you could run em and not worry about invasions stomping it with ease, you often have little to no reason to even bother with it in the first place, usually the colony having already reached max size and industry upkeep being a non issue to the player by that point.
it feels much similar to like if we had a hullmod that allowed any ship to gain a 360 shield BUT that shield has tripled upkeep and takes 9000% damage. like cool id love to have a 360 shield but the downside makes it totally unreasonable even if the only weapon you ever face is pilums and thumpers.
(edit): im not suggesting lessening the negative to the point where the dome is outright a better choice everywhere. I'm just saying in its current implementation its so bad that you really cant use it anywhere. pretty much its current form is the exact polar opposite of the issue you fear it might have if its downsides were too weak. It very much does not sit in any sort of middle ground.
like if i were to throw it on a world with defense on par with my faction's capital planet with the best possible defenses. that being 160,380 value on ground defense (size 7 planet with maxed out everything, seafloor cities, AND planetary shield). to get that value on a non-water world I'd probably need a size 8 planet actually, none the less, the value would be reduced to 8019.... I'm pretty sure I've seen size 3's with higher defense ratings, and definitely size 4's that beat that without even having max investment in defenses, said colonies of such sizes are also quite easy to invade, both for player and the ai, and you can't always guarantee the station on such a world is going to be operational cause random large attacks can happen, as well as operative sabotage. 95% reduction is incredibly debilitating, to the point that it would need some insane bonuses to even get considered by the player early on midgame colony wise. and of course, late game the player is just never going to bother with it cause they don't need the cost reductions from lower hazard, nor the growth rate, it's just not worth having to babysit the planet with defences weaker than tissue paper.
domes biggest bonus as of current is colony growth rate, this bonus falls off hard as the colony grows becoming far far less relevant, combining this with the gargantuan defense penalties and its just never worth it on any world, not worth it early on, due to it making the colony invade-able with a single marine, and not worth it later on cause the bonus's dont really do much any more AND the planet can still be invaded by a random pirate named bob with his lone hound when he saw that the hegemony blew up the station during a blockade. as far as i can see it, this will remain the case no matter what as long as the debuff is greater then 80% OR the dome suddenly has insane bonuses, which would just turn it into the "best on every planet" option you fear having it become.
dome would not be a super option even if it didn't have as bad a defense debuff anyway, as it would only make sense on worlds that have conditions it would block, say planets with extreme weather, toxic atmosphere, and thin atmosphere at the same time, the growth is a nice bonus sure, but most people are gonna avoid the negative effects it has even if they were far more tame then they are now.
(sorry for the text wall)