I have to agree with you that many people who vote third party do so believing that there is no difference between the 2 major party candidates, but on balance I would suspect that more Libertarians and Constitution Party voters are more inclined to vote GOP than Dem, if they vote at all. Just as Greenies are more inclined to vote Dem than GOP.
So you can not say that all or even most of those votes would have swung, but when you need less than 1,000 it seems likely you might get at least that. Also Coverdell/Fowler race tends to back up my initial opinion, but that is just one isolated incident.
I was engaged in an argument sometime ago regarding, for example, the Oregon Governor's race of '02, saying that had the Libertarian not been in the race, GOPer Kevin Mannix would be running for his 2nd term now. But as was pointed out, my assumption that those same Libertarians would've even shown up to vote absent a candidate for them and that Ted Kulongoski might still have won, might've proven in error.
The only bonafide contest I'm sure where a 3rd party cost us an office was when the rightist American Independent Party had a candidate in the State Comptroller race in '02 in CA. Mind you, it might not have been particularly important in another state, but this was the Tom McClintock race, and McClintock was the highest vote getter of any Republican in California that cycle, and had the 3rd party candidate withdrawn and endorsed McClintock, which would've resulted in a win, the likelihood as the sole GOP statewide officeholder at that time might've seen him become the "anointed" GOP recall candidate for Governor rather than the current RINO occupant.