Yeah the (what I personally call it) "choose your own adventure" style approach to Clojure projects, where you don't use a framework like Rails, but just string together your own project from separate libraries, is really both a "pro" AND a "con".
It's great when you know what you're doing, and indeed, I have my own personal Leiningen templates to set up a Clojure project the way I like it and to save myself some time. Bigger project templates, like Luminus, I often find personally aggravating because I often feel like it just barfs a whole bunch of unnecessary and semi-complicated (in my opinion anyway) code in a new project even with the most minimal options chosen. But that's the power of the ecosystem ... you can create your own project templates to meet your own needs.
But a new developer getting their feet wet in this ecosystem? Yeah, it is hard. And even if they use an existing project template like Luminus to bootstrap their project ... well, the project template only helps generate the initial project. Ongoing maintenance for updating dependency versions and keeping a working integration of the libraries it initially set up for you (with respect to newer versions and any API/config changes, etc) ... well, those responsibilities are all on you! Kit (another newer successor to Luminus) _may_ provide some better alternatives here, but it'll still be limited with exactly how much it can help here. But I think it's still much too early to say one way or the other with Kit, so who knows.
(Also thanks for sharing your Ruby/Rails perspective on REPLs. A colleague of mine made some similar comments to me when we were discussing REPLs a while back, and I've not spent any time with Ruby so couldn't comment. It's interesting to hear! Most other REPLs I've used outside Clojure were not too useful as anything other than quick toys for trying short snippets outside of the context of a full project.)