Yes and no. This is all spelled out in the post, but it's a little thorny.
Dune is a rename of Jbuilder (2016). Jbuilder uses Jenga (2012) configuration files.
> By 2016 we had had enough of this, and decided to make a simple cross-platform tool, called Jbuilder, that would allow external users to build our code without having to adopt Jenga in full, and would release us from the obligation of rewriting our builds in OCamlbuild [...] Jbuilder understood the jbuild files that Jenga used for build configuration.
So in 2012 it made sense for them to build Jenga, because there weren't any good alternatives - Bzl etc. didn't exist, so they couldn't have solved their problems.
And in 2016 they had open-source code they wanted others to be able build; those people didn't want to use Jenga, and JS didn't want to rewrite their builds so that they could use something else. Thus, Jbuilder was a shim so that JS could still use their Jenga builds and others could build JS' code without using Jenga. Bzl etc., even though they existed, wouldn't have solved these problems either.
