I think DS9 proved that ferengi are best as neutral counterpoints to Federation dogma.
Sorry but "neutral counterpoints" is gibberish. Also, "Federation dogma" doesn't make clear whether you're actually making a claim about the fictional Federation or expressing your feeling about the supposed "dogma." It is always comforting to see the poor judgment of anti-Communists confirmed.
The two quotes cited above do seem to be very symptomatic of the role of the Ferengi as artistic constructs. Tolerance primarily means respecting legal rights. Broader interpretations, which are by no means universally accepted, include eschewing driminatory practices in favor of the prevailing sect, ethnicity, party or nationality. The Jem'Hadar quote implicitly equating tolerance with indiscriminate liking, or even flattery, is rheoric, in the pejorative sense. The only reason I can see for taking it seriously as a pointed comment (instead of Quark spewing BS,) is a distaste for tolerance as such.
The quote from The Siege of AF-558 isn't readable as BS from Quark, but must be read as a shout out from the DS9 writers. That's a shame, because only blind prejudice allows one to insist that this is true. Loss of creature comforts has occurred many a time in history, but this quote misrepresents the experience of the past. It comes from willful ignorance and a reactionary disdain for humanity.