Wow. Those were some sh*t decals. I can't believe a pf restorer tried to pass that off onto you as an improvement. The decals are missing the white undercoat that is necessary for you to see the color correctly when illuminated from behind.
Most printers don't print with white ink because they are relying on the paper underneath to do that job. Try printing a color photo onto transparencies or overhead projector film and you can see what this looks like. What happens is the colors wash out. Commercial grade equipment can print white.
When redoing pf inserts that aren't' just black text you need to do one of two things. Either print onto a white material (which only works for inserts that have no transparent areas), or print a white layer underneath the colors.
IJ has quite a few inserts with colored ink that have no transparent areas, but not all of them. Well of Souls, Castle Grunewald, and Steal the Stones have clear areas, and I believe most of the faces have clear areas as well (whites of the eyes, teeth, Dr Jone's glasses frames)
They would need to knock all the inserts out and redo this with a better set of decals, or lacking a better set, redo it with a new set of decals but airbrush on some white on the inserts prior to putting on the decals. Which inserts did they "fix" in the game? All of them or just the 12 modes?
I have turned down restoring a IJ pf that had insert damage on the faces because of this exact problem. Without an accurate set of decals you are not going to make it look as good as it was originally.