... but we have only seen glimpses of two that appear to be harsh wastelands...
I'll concede that canon is on your side here, though I think the canon could have been better thought out. We did see a lot of hellacious colonies. You'd think that the goal of every race would be to build a comfortable, prosperous "New Earth" or "New Romulus" but we never saw one.
I'm not sure if a fictionalized supernova counts as a plot hole. I mean, human/alien hybrids like Spock are just as impossible, as are transporters and Genesis devices. They're just fantasy elements.
The problem is that they didn't fictionalize it, and the viewer is left to assume it's an actual supernova. If they'd said "supernova enhanced by alien technology," that would be different. The other fictional elements listed are clearly the product of imagination. The writers needed to toss in some sort of qualifier, but they dropped the ball. I know I had a wtf moment when I heard Spock say a supernova would destroy the galaxy.