A question (without answer, closed, but not deleted) with score -6 (and 1 spam flag) does not appear on the MO frontpage even if by its "age" it should.
To some extent this indeed supports what you said (and it was not my intention to invalidate anything you said), by contrast I wanted to continue and confirm my original claim (and answer of your question) whether or not score has an influece on the presence on the MO frontpage:
I am convinced score does have an influence.
As I see no other explanation for this observation; the question was not delted and still has only one flag [turns out two by now but then it had one, also meanwhile score - 7], and one flag certainly does not suffice, so it ought to be the score. (By contrast deviations from the [rough] principle I postulated seem reasonable explainable by things Emil J points out.)
Final note: the question I am talking about is the one in the "trollery" thread; so it might be delted (and have more flags) by the time you check; but on the other hand the timeline shows it was not delted when I made the forst comment nor is it just now (except it changed in the last five minutes)
]]>Thus, I am now (again) convinced that the score is (also) relevant [though the details are not fully clear to me], as a single flag certainly does not make question dissapear. Further details: the question had no answers and was closed; this might play a role; the one -8 counterexample I remember for example had an answer.)
Sorry for bringing this up in a way that you'd have to take my word for it, but when it happened meta was down. (I can mention the question of course, but it would not really help as now it is to late for observing it and I do not want to draw particular attention to it; but if you really want to know look for one where I left numerous comments recently [I did not vote it though])
]]>http://mathoverflow.net/questions/130552/watch-iron-man-3-movie-onlinedownload-iron-man-3-movie
]]>Kidding aside, this is a possibility but chances are it would be an annoyance for 'everybody' [I am now not that convinced it would not appear] and in any case it would not completely answer the question I have if it appears [as I could imagine, whatever the situation now on math.SE that actually an edit overides the dissapearnece; else, given the sorting-categories here it would be virtually impossible to ever again give any visibility to downvoted question].
While abstractly I am quite courios what is an is not the case, and entertained the idea (and even started) to test this on the test site (but gave up and deleted the start soon when I realised I'd need a couple of accounts past 100 points which then seemed a bit too much effort to create), in the end I think it might not be worth the effort to now figure out what is the case on MO now, since anyway in only a couple of weeks (or so it seems) it will be as on math.SE. (Where, if I understood you correctly, my original statement would/will have merit, while possibly/likely being wrong at the moment.)
But all in all, what I consider as most likely at the moment is that the flag-dissapearence exists, while the score one does not, and I just got confused regarding this (as until not too long ago I did not see the flag-count but only the score and noticed questions dissapearing, possibly in combination with reading something over at SO and not paying enough attention that this is/might be a 'new' feature).
]]>Added; Or, it disspears (only) if there are a couple flags already, and I only thought it was the score.
Added 2: the following answer by Jeff Attwood mentiones the dissapearing feature on SO at Aug 30, 2010 (thus already long ago and it was not introduced then but existed; meanwhile things are quite different, interesting vs active or something) which somewhat support the idea this would exist here too
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