Thank you so much for all the information! I have DVDs of Boogiepop and PHO so I will have to inspect the scenes with those cels more carefully. I do know that there were no overlay cels, and that these are in fact the ones in the shots.
Interestingly, I did not bring up this cel, but I think it fits with one of the possibilities you mentioned:
http://cat.rubberslug.com/gallery/inv_info.asp?ItemID=107138
This cel has a second layer with the pink areas on another cel. I have not seen MKR in TV or OAV so I don't know what is happening here, but I suspect some kind of light effect was used. (If anyone can tell me which this cel came from and my Fuu too, I;d appreciate it. I have them listed as TV cels but I suspect that they are really OAV.)
I have one other partly painted cel which is really interesting:
http://cat.rubberslug.com/gallery/inv_info.asp?ItemID=85339
This cel of D has a fully painted face but his hat and a lot of the black on the cel comes from the paper underneath. I found this cel in the movie and it is authentic (It also has the studio mark). There is a swirly special effect occuring in this scene that partly obscures D. I thought originally that the black was not painted because there is so much of it that it made more sense to use paper. (The cel would be so stiff and heavy and apt to adhere to things.) I wonder if the fact that there was a special effect used in the scene had anything to do with it as well?
I wish all cels came with timing sheets, or some explanation as to why things are as they are, but I must admit, it is kinda fun to search for answers yourself. Some things however, are simply beyond my limited knowledge of animation production, especially regarding special effects.