Sure there are two types (or more?) of dependencies, but at the end of the day the AppSignal app requires those +13,000 dependencies in order to work properly (first to build it, and then to run it). That's horrendous.
I believe all pieces of technology have similar dependency graphs.
In the same way, the "dependencies" required to build my hardware aren't counted in that number. What counts is the extra stuff that isn't already part of the running system.