Another interesting scenario, though I am sceptical as to whether it would really have been achieved. If the margin of victory is slim, which it sounds like it would be, fundamentally changing the direction of the country without a firmer mandate would be risky. Furthermore, what is the position of USA going to be? Sure, in a 60/40 split they'd probably reluctantly concede, but a 51/49 split I suspect will meet with their resistance.
Chen won 39% of the vote. Song won 37%. Lien Chan (who warned of provoking the PRC's wrath if Chen won) won 23%, with the remainder between minor candidates. Song and Lien were both formerly of the KMT, but the KMT was so wracked by infighting that Song resigned and ran as an independent candidate. Lien had never held elected office and was widely seen as out of touch and aloof. It's also widely believed that then-KMT President Lee Teng Hui secretly sought to undermine his own party's campaign in order to elect Chen, who shared his pro-independence views.
So if Song won, even by a narrow margin over Chen, then the fact that pro-unity candidates won over 60% would be a strong mandate for his cross-strait policies.
If the PRC is confident that the Taiwanese voters accept being Chinese, though disliking Communist Party rule, it may well agree to an informal non-aggression pact so long as that consensus remains (and Taiwan agrees not to host covert US spying, to "eventually" work to full political union, etc). Relations across the strait will be much better than between the two Koreas, or even between the two Germanies.
A clear democratic win didn't stop US displacing Allende in Chile, true it was a different time, but ......
Seeing the US didn't interfere when successive South Korean governments (tried to) reconcile with the North in the 1990s, I doubt they will care if the Taiwanese decisively vote a certain way.