(I work at Stripe.) What it even means to have a "merchant account" is shifting in the industry, so it's hard to be absolutely definitive, but: most of Stripe's transactions run through what would traditionally be designated as regular merchant accounts. At the same time, it's our belief that it shouldn't matter (which is why we don't expose this). There are properties that our users should care about -- that funds are held in their name, that the right thing appears on cardholders' statements, etc. How that's accomplished is an implementation detail that may change over time and which will depend on the payment instrument, country, and so on.
This part of the process seams especially opaque and I've had far more customers than I would have expected have cards declined for no discernible reason.
I wonder if shared merchant accounts are a plus or minus here.