Sorry to hear that you had all those troubles. Regarding the Ghostscript, I brought it up here Juliaup breakes GMT (via Ghostscript and tmp dir permissions) but it went up unnoticed. I must report it as a bug.
Hmm, can you elaborate a bit more (or open issues i GMT.jl repo)? GMT has only 2 non-stdlibs or *.jll.: Tables and PrecompileTools, so a very minimalist depends chain. What do you mean by: transient dependencies?