What do JoeTang's calculations really mean?

I see what you mean, thank you for replying. I still don't know if there truly is a difference between classes in terms of damage, at different aspect. E.g. at different level of funding, the potential maximum damage, etc

Oh, there definitely is a difference.
It's easiest to see at the top end: when you're capping all hits, the class with the most hits-per-second can dish out more total damage, pure and simple. That's why you see certain classes dominate Dojo, and why Marksman Bryan was unable to defeat Dorothy within the time limit as a Marksman, but could do it as a Bowmaster.
As for differences at lower levels of funding, they exist but are harder to see. JoeTang's chart can tell us that at, say, 100k range, class X can do more damage than class Y. But the chart doesn't tell us how hard it is for each class to reach that 100k range (different weapon multipliers, etc) and definitely can't tell us how things like mobility, stance, avoid, range (the distance kind) affect each class's mobbing or bossing abilities.