Could this be a misunderstanding caused by different understandings of the meaning of the word "accidental"? Simon, by "accidental", do you mean any change of pitch of a note, whether indicated by the key signature or not? If so, that may not be the way readers of this list normally understand accidental. Take a look at a simple score with any key signature other than C major or A minor. The only accidentals that are marked in the score are those that depart from the key signature. It looks to me like Lilypond's default mode would replicate faithfully the accidentals (and only those) which you have circled on the score.