I mean, he said nothing of the sorts.
You complained about Empire Size, and in response it was said that, played competently, even an empire with size 3000 can rush through the tech tree. Nobody said you're not playing competently by not having an Empire of that size.
You then said that you must be competent at the game because you can generate thousands of research with just one planet, which was rightfully concluded to be a pointless claim since nobody knows what mods you're using. For all we know, you might be using a mod that just adds 5k research to your Capital. But as said before, your competence was not questioned anyway.
And yeah, if you play modded in a way that allows for you to have a single planet and generate thousands of research on it, then your opinion on game balance is also rather pointless, since it's highly unlikely that you could draw informed conclusions about the unmodded game with such mods active.
All of that being said, I think there should definitely be ways to create generalist planets. In my opinion, that not being possible is probably the main downside of the new zone system as it stands currently. Not too relevant for "normal" playstyles, but I think the ability to deviate from "normal" play should definitely be there. Though, if you're playing heavily modded anyway, there'll probably be a mod to achieve that once the patch has been released.