By default, is.opaque returns a single logical value.
If single.flag is false, it returns a logical vector/matrix/array matching the dimensions of cols.
By default, standardize.cols returns a character vector/matrix/array matching the dimensions of cols.
If as.list or as.array are true, it returns a list or array, respectively.
In lists, each element corresponds to each channel, and in arrays, the last dimension corresponds to each channel.
vt3.prep.cols returns a length two list, containing the opaque flags and the standardized colors.