No, I think you misunderstood my point. Any command you type after pkg> is run in the environment pkg, and therefore will not affect the Pluto notebook, which generates its own environment. E.g. if you did
pkg> add DataFrames@1.0
in the REPL, then
julia> using Pluto; Pluto.run()
and then put
using DataFrames
at the top of your notebook, Pluto will automatically install the latest DataFrames version (1.2) in your notebook environment, and you will be using that version in the notebook, not the version in your pkg environment from which you started Pluto.