colored placement of the components

Your "demo file" looks like somebody took a black&white assembly 
drawing, imported it into a vector graphics software and painted 
half-transparent polygons over the existing drawing.

I don't exactly understand what you mean with "How could we (...) give 
then reference designator".
The reference designators are defined by the engineer drawing schematics 
and desinging the PCB. The text sitting centered to the colored polygons 
also seem to be drawn later on in the vector graphics software.