Think about cars for a minute. Don't they all look and function the same? Where's the steering wheel? Where's the radio? Where's the motor? Gas pedal? Brake pedal? Seat adjusters? Cup holders? A/C and heat controls? Doors?
Most cars are pretty much the same. The differentiation is in the paint colors offered, the design of the body, wheels, and rims. The visual aspects, per se.
You see, the same thing could be said for start up sites. Everything is where you expect it to be. What's different are the logos and color schemes used.
Don't equate using something that works with following herd mentality. The reason something like Bootstrap by Twitter is used so often is because it "just works". If you are a start up with limited keystrokes before you burn out of money, then you focus on other value-generation parts of the business. I would rather get a halfway decent Bootstrap looking site (with tweaks) than spend money on a designer or time creating something that is different but I have no idea if it will convert well. In the meantime, I'll spend my time and energy on building new features. If the idea proves out, we'll loop back on the launch pages and do some A/B testing after the fact.
Maybe websites that have been around for a while tend to fall into certain design patterns, which may be a reflection of bureaucracy or other patterns that structured orgs fall into.
What looks like a startup website is merely the lack of that. Just a thought anyway.
While that unique brand and vision is unclear and unrefined, the closet substitute likely to be "right" is the average of what everyone else is doing.
Do you have any examples of a startup that does not follow this standard format?