If your customers are mostly designers who get snooty about that kind of thing, you run some risk. Otherwise, most people probably have no idea at all what it is, as long as it looks and works ok.
Differentiation is never a bad thing. A basic bootstrap layout connotes a project in beginning phases typically. For example, Coinbase began with bootstrap to get a product out quickly but moved on once they realized that for people to trust them with large sums of money/bitcoin, they had to appear more established and professional.
When I see a website using default bootstrap styles I think it's fleeting and not worth of my time and money.
When I see a website using default bootstrap styles, I give the service/product a test run and see why the reason I came to the site originally was a viable thing for me to continue. If not I don't waste anymore time or money.
But hey, you're choice to spend your time and money on anything you want, and if something is usable but not exactly custom pretty, your choice to not use it.