The author has a point - one I don't sympathize with much, by the way - and he's explaining it clearly. His reward? An alarming number of commentators here on YC smugly calling him an idiot and repeating with tedious condescention the standard talking points on freedom, gratis, etc., advertising nothing much beyond their lack of reading comprehension and a healthy knee-jerk reflex.
I do genuinely think that there are two different costs for software-- the cost to the programmer and the cost to the user. The two costs have no relation to one another.
I agree that you and the original author are both talking about the cost to the programmer when you say that "free software" is not really free, in that the programmer bears an opportunity cost, as you described earlier. That's true. You, the original author, and I all agree on that point.
Where we disagree, I think, is about whether that cost is important. I think that proprietary and free software have roughly the same cost to the programmer, i.e. it takes just as long, just as much effort, to write code, regardless of whether you're getting paid. Since the cost to the programmer is the same for both, it's not a distinguishing feature of free software.
If he just means that there is a cost to create all software, it's an obvious conclusion. I don't think I've ever heard anyone claim otherwise, i.e. that free software is created without time and effort by programmers. That's why I don't find the original argument compelling.
[1] Hard to do well. It's pretty easy to make vague assumptions and proceed from there.
You're correct that there was an opportunity cost for me to write the code. I spent a few hundred hours on it, when I might have been programming for money. Fair enough.
But when we talk about whether software is free, the question is either how much is costs to use it (i.e. is it free as in beer?) or what license it uses (i.e is it free as in freedom?).
In this case, the cost to you is $0-- free as in beer-- and the license is the GPL-- free as in freedom. (Perhaps we can omit the GPL vs. BSD argument here.)
A better counter-argument might talk about the opportunity cost for you to use free software.