I suppose you could argue that the tax system should be aware that common stock valuation should not be inferred from preferred stock valuation...
Sure, employees share some responsibility for accepting compensation that includes stock which can be sold on your behalf without your having any say in the price you're willing to take... but companies choose to offer comp packages which include that kind of stock precisely because it's hard for employees to value, and it's easy for employees to overvalue.
You're mistaken here. Your point rests on there being a possibility that Blackberry paid the same amount for the company (the valuation), but common stock holders got more (the waterfall). This was not possible.
They also could not have changed the waterfall. So I'm not sure what your point is, really
(And it kind of is the startups fault that there isn't a way to exercise-and-sell the options. If it was a public company you wouldn't need to take the risk of a massive AMT bill)
But, if the company heavily compensates people with an asset that has irrational tax laws, then it does seem like they bare responsibility.