Regarding your second sentence, who says that would be a bad thing? I'm a little confused about the situation you're describing. Most analysis of voting systems I've seen isn't concerned with the fact that valid candidates may be left off the ballot. That's obviously an important consideration in real elections, and if there are primary elections the choice of voting system there obviously matters, but in the final election it doesn't seem particularly relevant.
Similarly, if an election has a Condorcet Winner, and adding a candidate creates a Smith Set (thus potentially violating IIA if a certain candidate is chosen in a "tiebreaker"), this is not necessarily a bad thing.
If that happens it means that people always legitimately had those views, and were not able to properly express their views by choosing among the more limited number of candidates.