How do I differentiate outliers from in-group variations in a DESeq2 PCA plot of 9 samples distributed into 3 conditions?
Since you have so few points here, it is hard to tell which are outliers by just looking at the PCA plot.
I suggest you use correlation heatmap for your gene expression and check whether there are obvious outliers.

As for using more than one groups when plotting PCA, I think you can just try passing a vector with many groups to the argument intgroup.