I think OP is trying to point out the fact that we are considering the price of bitcoin against USD and we should not be doing that! What OP says is that, we should not be doing that, instaed we should derive the price of a commodity in bitcoin unit only!
Bitcoin has not yet reached that stage. I am an early adopter of bitcoin and way more devoted to it than a lot of people! But bitcoin is not accepted enough when we can actually do that. It has not yet become a global standard! It's just 10 years old only! Give it another 20 years of time, probably we will reach that stage where we will derive the price of any commodity in bitcoin unit only!
No matter how great we understand Satoshi's whitepaper, we don't really have a choice!
I don't think OP means that at all, he's talking more about the fact that most people choose to hand over control of their coins to exchanges.
Well that's at least part of it, combined with the fact that we use exchanges in the first place to buy and sell Bitcoin.
I'm personally pretty pragmatic about it, I don't mind buying coins from exchanges. After all, it's usually less risky than doing P2P trades and you often get far better rates, depending on which exchange you use.
The only thing I really worry about is too much power going to one specific exchange. That's why I tend to use the smaller exchanges which have proven to be secure, Kraken is one of my favourites.
That said, I do also buy goods and services directly with Bitcoin and I do try to find services which don't immediately exchange their BTC to fiat.