Speaking from play experience, the stock system is the way it is to provide an ending point. If you had to have full cash value to buy someone out, it would take a long time to reach that point in a close match. Both players would gain cash at roughly the same rate while trying to buy out the other, making it impossible to have gain enough cash to actually win. Also, reducing the weighting of cash on the stock value alleviates large fluctuations on stock value as cash fluctuates over time. It's also difficult to have a proper company valuation because how do you accurately value the buildings. claims, etc?
It's not a true stock/value system because its designed to facilitate winning more than anything. It wouldn't be fun if you had to have enough cash to cover cash + assets because the game would get drawn out too long. Ultimately, had you ended the game when you should have, it wouldn't have become an issue.
Sorens spoken about the stock a few times in various podcasts posts and interviews if you want to dig them up to get a better idea on the role stock plays. I suspect internally they have played with many different models, a few have ended up in the various prototype phases. Although the current model isn't the most realistic, modern stock market prices are mostly a load of crap and hype anyway.
BTW, hover over the colony icon next to the stock price shows assets, cash and debt, so you can see how much cash they have.