One thing you could do is creaye a symbolic link to change the directory. For example, I have a symbolic link for ~/.juliarc.jl to the file ~/.julia/config/startup.jl in my home directory. Originally, Julia had the config file names like that, and I like to continue using it there, so I simply created the directory symlink to it.
Sure, a symlink is a good workaround in some cases. But that doesn’t help if, e.g., you want to completely separate Julia installations (resp. test instances) and can’t use VMs/containers.