Julia 0.6.4 creating ~/.julia/lib/v0.6 even when external JULIA_PKGDIR is specified

I want to use both Julia 0.6.4 and Julia 1.0 in my Linux system (Elementary OS 0.4.1, based on Ubuntu 16.04).
In order to isolate 0.6 from 1.0, I created a dir ~/.julia-0.6/ and modified {JULIA_DIR}/etc/julia/juliarc.jl to include ENV["JULIA_PKGDIR"] = "/home/vish/.julia-0.6". Now if I start Julia (specifically calling 0.6.4 binary) from terminal and do a using <Package> at REPL, it creates ~/.julia/libs/v0.6 and creates some *.ji files init. However, if I disable that line in juliarc.jl and instead call julia with JULIA_PKGDIR=${HOME}/.julia-0.6/ <path to 0.6.4>/bin/julia, the lib gets created inside my specified directory only, instead of ~/.julia.
I want to use the solution with modifying juliarc.jl files due to some IJulia requirements (Can’t specify a ENV VAR in kernel.json to make the other solution work!!).

So is it possible to specify the JULIA_PKGDIR in juliarc.jl and still make julia generate lib inside the specified directory?