I don't think normal people would even notice this. Doesn't mean personalization isn't something that should be done, just thinking you might be overblowing the problem.
I disagree - their target audience is developers, not "normal people". Because bootstrap's default styles have been beaten to death by startup-in-a-weekend type apps, I subconsciously don't trust their service because it seems like it might not be here in a month or two.
Say what? That they won't be here in a month or two? I think they definitely will be around, they seem to be ripping up HN lately. All I'm saying is that using bootstrap's default styles tarnishes the brand they are trying to build (which is especially important because their target audience, developers, are very familiar with default bootstrap).
I do already see some general design improvement on this page compared to some of the earlier ones, good work on that! As for obvious Bootstrapness, I think if you wanted to do something quick & minor with a big impact you could just change that default navbar background.
As it stands it makes the site look very backwater, regardless of features.