For now I’d advise not to use b0caml, it was written with assumption that a simple directory-based notion library would make it upstream. But that never happened, so it likely needs adjustements to be more compatible the dreadful status quo.
I think the best way is to do what what you suggest: use ocamlfind. The advantage is that you will also find the ocaml/ocamlfind combo in the system packages of many linux distributions. ocaml could have been an excellent system “scripting” language but, as usual, totally missed on providing the integration mecanisms and experience that would have been needed to do so.
Also if you don’t compile them like b0caml does you may want still want to check that your scripts compile correctly for which you can use this hack and of course the merlin issue remains. Yes all this is clunky beyond sadness but people mostly don’t care about things that do not fit the narrow minded dune narrative nowadays.