Is dune just for building targets, or can I also make it organize build output?

Have you tried GitHub - diskuv/diskuvbox: Basic, cross-platform set of commands to manipulate and query the file system, and OCaml library. (see also [ANN] diskuvbox: small set of cross-platform CLI tools)? Its purpose is to provide a small set of command-line tool helpers in a cross-platform fashion to avoid depending directly on an Unix shell.

Cheers,
Nicolas