Long story short - thank you Tilman, I found a solution. I am creating transparent PNG directly now. I had to solve the problem of loading it to PDFBox, while it will preserve its transparency, by using ImageIcon as a reader, from which I can finally create a proper BufferedImage with type INT_ARGB, which PDFBox has then no trouble displaying as a transparent image.
btw I don't know how to respond with keeping proper quotation of message to which I am reacting, sorry for messing the thread up.
