How does PGS select or distinct the colors?

First of all PGS makes a distinction between the different methods like the color models: RGB, CMYK, Pantone, and so on. Even if it is the same color! So Blue.1 and Blue.2 could be the same color only in a different color model.

Then in one color models, like for instance RGB, it takes notice of the percentages of each color (R and G and B). Are they a match then its one color. Do they differ, if only a little bit, then the color has that name plus a dot and a number, for instance Red.1. The next one will be Red.2.

If somehow a color is missing because it is deleted then PGS (5.0.4.4) acts differently.
An object, not a text object, will turn black (fill or line). It will be named <custom>.
A text object with a missing color will crash (freeze) PGS 5.0.4.4. It may be a color not in use (unchecked in the Line & Fill): PGS does crash. Bug #215/217.

PGS does not make a distinction in a name So Red can be Rood (Dutch), Rot (German) or Rouge (French).

I like to add that within a color model, say RGB, there is difference, for PageStream sake, between a process color and a spot color. Even if the color is the same!