This is nonsense. Stock vs flow comparisons occur all the time and no one is confused. How often have you heard things like "Don't buy a house costing more than 3x your salary" ? No one objects and says it's illogical to compare a fixed cost to a rate of accumulation.

The comparison is straightforward: If a country with a trillion-dollar GDP could put all its useful effort into constructing a company, they'd produce a company like Apple once a year.

Is that some kind of insane conflation? No one thinks it's actually possible for a country to produce a company as an output. It's just a way to describe the approximate order of magnitude of two things - the valuation of a company, and the yearly output of a nation.