So, you could use AlgebraOfGraphics to generate the correct Makie boxplot as follows.
julia> using AlgebraOfGraphics, CairoMakie
julia> set_aog_theme!() # optional
julia> df = (x = rand(1:3, 1000), y = rand(1000), group = rand(1:2, 1000));
julia> plt = data(df) * mapping(:x, :y, color = :group => nonnumeric, dodge = :group => nonnumeric) * visual(BoxPlot);
julia> draw(plt)
Doing this plot directly with Makie is a bit clumsy at the moment, but I’m planning to make a PR to support passing a vector of colors (see examples with violin, where this is already possible).