My answer is in four independent parts:
a) I think a Skeptic flag is a good idea for the first benefit (Makes it easy for the newcomer skeptics to find preexisting skeptical questions).
b) If the intention is to help some people avoid reading skeptical questions, then I feel it is not such a good idea.
c) "Skeptic" is arguably a negative-sounding label, not unlike "Cynic" or "Doubting Thomas" or "habitual critic". It sounds like you are labeling the person, and not just tagging or flagging the question; this is somewhat similar to having a "beginner" flag. May I suggest a "Critical Reasoning" flag or tag instead? Or maybe "scientific temperament"?
"Skeptic" seems like labeling the person rather than the question -- rather similar to having a "beginner" flag. It may be worth avoiding.
Instead, consider introducing a "Critical Reasoning" of "Scientific Questioning" flag. Or maybe, "Secular Buddhism"?
Simultaneously, consider having flags to indicate a complete and unquestioned belief in the scriptures. How about "Faithful Disciple" or "Literal Faith"? This might discourage skeptical or non-scriptural answers (or non-literal interpretations of the scriptures) from being attempted to questions thus flagged.
With such flagging, one may possibly reduce incidents of skeptical or critical questioning offending faithful/literal followers of the faith. It would be like saying, "Viewer discretion is advised. You have been warned. Proceed with caution." If, after reading this flag, someone feels offended by the question, it means that he/she has actually gone out of his way to read the question in order to feel offended.
Vice-versa, it may reduce the incidence of the faithful/literal followers feeling that they are being trolled by persons with a skeptical outlook. Because anybody who deliberately goes to questions marked "Literal Faith" and leaves skeptical answers or questions could be marked as a troll.
Questions that have neither flag would allow interactions between skeptical persons as well as literal followers.
d) How about introducing flags to indicate diametrically opposed qualities also, such as "Fundamentalist" to indicate total belief in the scripturesFair enough? This would have the benefit of enabling some people, who may want to avoid discussions about hell, hungry ghosts etc, to just avoid reading those questions.