I disagree. It's more comprable to if they used WordPress instead of Ghost. The database is a few layers further down, whereas Ghost is basically 90% of the end product (not sure how much they've adapted, but looks like a lot from John's Tweet)
Substack is positioning themselves to their customers, which are journalists/authors, as a comprehensive alternative to having a normal job working at a newspaper or magazine. That seems to include high-touch customer support, an integrated business model with payments, a mailing list system, a distribution method, etc. It's more of a service than a piece of software.
Ghost actually seems to have jumped on Substack's bandwagon by trying to skew their blog software toward being a direct Substack alternative.
So Ghost seems to have adopted Substack's business model and Substack seems to have adopted some of their blog technology.