Ah, also missed the details on the startup.jl in the original post 
@oheil is right, the startup.jl in the Julia specific folders is not the right place to add modifications, in general with Juliaup you should consider everything inside the ~/.julia/juliaup folder as managed by Juliaup and you should not modify anything there by hand. ~/.julia/config/startup.jl is the right place to put your own custom startup code into. If you want to do different things for different Julia versions you can just use a if VERSION block in the startup.jl.