All goals must be completed within the same quarter. That's why the numbers indicate what you achieved in the previous quarter: It's basically the win condition from the previous quarter. Also iirc there is no timeout for the cookie.
About the cost for funding industries, you can use the "Base cost mod" NewGRF to adjust them.
Wrt. the goals for different companies: If there would be a new version, I would likely remove the option to play with anything other but "secondary" industries. The primary industries case does not work particulary well, since you mostly have to fund industries instead of transporting stuff. And well, the case "primary and secondary" is completely broken, since the goal cargo amounts are not comparable at all. Anyway, maybe I can figure out a method to distinguish secondary and tertiary cargos.
About the starting amount of industries: Does that really matter so much? In Silicon Valley you do not have to start early with the goals. You can very well make 5 years only money with completely different things, and then complete the goal within a quarter (if you build fast enough). The cargo amounts transported are not accumulated as in NoCarGoal. Only one quarter matters. Basically, rush for money, not for the goal
Story book would be a nice thing, but you can already now see the amounts of competitors by opening their goal windows. Hold the mouse button on the goal menu for that: It's the same as for the other menus.