My own organization is a nonprofit startup. Our 501(c)(3) application took four and a half years in review. During that time we had no final status so rule out most foundational support and as a nonprofit there's no equity investment either. Essentially we had to scrape for what help we could find little by little without much to offer in return. Luckily we're in a high-profile space (music) so we could return enough PR while building.
The IRS eventually denied our application for status. It's not uncommon, especially in the open-source space, but luckily we now have a major law firm representing us pro bono, we hold credible domestic nonprofit status (at the state level) and we've build up enough of a reputation. We're still cut off from most grant-making, but we're finding ways to be creative.
My point is that the administration of the organization itself is no trivial matter, and it's especially difficult to carve out a space for yourself as a nonprofit if you don't fit a traditional nonprofit mold. (And innovation in the nonprofit space is vital — both in the models and the regulation. Sadly the latter lags behind.)
Not a complaint at all, but I'd definitely argue that the differences are many. And for nonprofit startups without a 501(c)(3) you're going to face a challenge, even if you're supported by a fiscal sponsor. It's similar waters for sure, but a whole different ocean.