I disagree. You overlook the value of incumbency.
Good players frequently sign extensions with their current team. "We like your client. We hope he likes playing for us. Here is a market-correct offer for X years, covering his last year of arbitration plus X-1 years. It's possible he could squeeze out an additional $X million by going through free agency, but our offer removes all the risk involved in going that route. Please give your client our warmest regards, and let us know what you and he decide."
Paying market rates for players is more expensive than paying for young talent. But there is a value in "we have him, and you don't," for players like Berrios who belong, at worst, in mid-rotation for a championship-caliber club and possibly #2 or even #1 in specific cases. No team wins awards for the most efficient use of budget space - you use the budget space you have (or are comfortable with) to amass talent.
The Twins obviously were not going to make an offer Berrios was willing to accept at that time - that was clear from every report seen in the press. So trading him for high-value prospects made sense for them. But the Jays were operating on a different plane and such a trade made sense for them in a different way. They traded prospects for 1.33 years of current control plus the chance for more.
It turns out $131M was the Jays' commitment. If seems entirely plausible the Twins found such a number way too rich for their blood. The trade made sense from both sides, and with a chance for a time-window much longer than the nominal 1.33 years of remaining control. And I think it's entirely fair to count all of the WAR he's given the Jays.
It kills me that the Twins can't commit $131M to one of their home-grown stars.