Regarding score, it's also worth noting that a lot of industry folks felt Sondheim was robbed for Sunday in the Park a few years earlier. Meanwhile, Webber had won twice in the last 8 years, so crazy as it sounds, Sondheim actually had a bit of an "overdue" element working in his favor.
Would have been interesting to see which would have taken Orchestrations had that category been around. On the one hand, the Tonys love awarding big grandiose orchestrations like Moulin Rouge, American in Paris and Light in the Piazza. But they've also awarded orchestrations for plenty of smaller, more intricate scores ala Assassins, Next to Normal and Evan Hansen. So a real toss-up there.