James Loxton has a post at The Monkey Cage about "authoritarian successor parties" (parties that emerge from authoritarian regimes but continue after the transition. Using Keiko Fujimori's loss as a starting point, he notes how strong ASPs are globally. And generally, this doesn't matter much, which is a good thing.
ASPs may even have some positive effects on democracy by helping to include former authoritarian incumbents in the new regime (thus discouraging them from becoming “spoilers”). This could inspire autocrats elsewhere to initiate their own transitions to democracy by showing that there is life after dictatorship.
I think this point is the most salient. Negotiated transitions are facilitated by promises of future participation. This is also how you get rebel groups (like the FMLN and perhaps eventually the FARC) to lay down their arms and join the political system. If you block that participation, you're asking for trouble.
At the same time, there are lot of apples and oranges. Chile's UDI was a strong, institutionalized party (which, incidentally, still has never won the presidency) whereas Alberto Fujimori was a personalist leader without a true functioning party behind him. There are also, of course, different kinds of transitions. Fujimori's flight from Peru bears little resemblance to the electoral loss of the PRI in Mexico.
But an interesting topic, and I see he is working on a book, which should be worth checking out.