Hi,
The colors you define are not for the different groups, but for the confidence intervals of the box plots. Let's look at this example I made:
siberDensityPlot(SEA.B, xticklabels = c("group 1", "group 2", "group 3"),
probs = c(99, 75, 50, 25),
ylab = expression("Standard Ellipse Area " ('\u2030' ^2) ),
bty = "L",
las = 1,
main = "",
prn = TRUE,
clr = c("red", "green", "blue", "orange")
)

For illustration, I choose the confidence intervals to be displayed as 99, 75, 50, 25 (see probs parameter). I gave each of them a different colour. As you can see, the colors correspond to the same confidence interval in each boxplot, and this help comparison between groups. Coloring the different groups in different colors would not make sense as you loose the visual aid for comparing the same confidence interval across different groups.
Hope this clarifies it
PJ