Why Nova's Automated Refineries are more expensive?

That was the argument of your grand-grandfather.
Zeratul has been released since then, so the argument is completely obsolete.

even if it costs 125, i’d rather have it automated than wasting 12 supplies out of 100 pop. ppl say it is unfair or unjustifiable compare to vorazun gas, but i didn’t know nova was supposed to be vorazun twin. why compare just one aspect/feature of a commander to other commander while completely ignoring the commander as a whole?

Probably cause Nova starts off way more OP than Vorazun so they balanced it out by having more expensive refineries. Not saying it’s right but that’s probably why.