I totally agree with you. I always had the policy of giving 120% while working for someone, despite if I liked it or not. I always wanted to give a final product of quality and this is actually what gave me more and more job with time (and pushed my workflow and technique much further).
I agree with you about the fact that this technique of counting may not apply so well because of all the time consumed by talking with the clients and advertising, etc. But we can fix it in two ways:
1. You count that time as well as part of your job (which I encourage you to do).
2. You don,'t. (which I also encourage to do)
See, you are in your full right of counting all the time invested in your work. But in the end we still live in a capitalistic system (thankfully not in Steemit) and we need to give some part of our work away. This is (unfortunately) what drove me so far and stills do it! For example:
I had all June filled with work from the beginning to the end. Work from a client from Argentina, and I was asking him for budget according to the prices in argentina (using the knowledge that they wouldn't probably know how much living costs in Poland, which is fair because they would be aiming to pay with argentinian charges, so it's a win-win). But in the end, one of the 7 projects I was leading as concept designer was so long (and I will make a post about that, was for Raid) that in the end I understood that they wouldn't have the budget to pay me if I would keep the numbers that way. So I decided to start discounting by quantity to keep them hooked.
So as you can see, sometimes giving part of your job away, represents (sometimes) a good benefit.
What I am trying to say, is that there is no perfect formula for this. Also, it can vary a lot from the quality of the product you have and for that you should leave your ego behind, which is also hard being an artist (because the ego drove the artist in first place to do what he does !).
From your actual skills, we can tell that you gave 120% of you! Thanks for the example you reported, probably it's just a matter of "reading the game" sometimes! And there's a lot of factors involved; the client type, your value, if the client is giving you a lot of work... so in the beginning it's not easy to set a price properly but I guess with experience this will come easyer! Anyway I personally found very helpful to do an estimation based on "work per hour" as you do, to have an idea if you are completely wrong or your on the way!