Until "Come from Away", yes, that was a possibility, though since "Great Comet' can't tour, it was a long shot. But once "Come from Away" appeared, it became a two-way race between them. I still thought Dave Malloy and Rachel Chavkin would walk away with Tonys for Orchestrations and Direction, respectively, but I don't recall any predictions that "Great Comet" would stage an upset.
I do recall reading about a possible race between "Passing Strange" and "In the Heights', particularly in the writing categories, which somewhat seemed to come to pass. It helped that "Passing Strange", unlike "Great Comet", looked good on TV, which created a sense of excitement around the show as it made the rounds performing "Keys/It's Alright".
I'm forever grateful that we have the Spike Lee film of the original production, which remains a very good record of the show, and has kept it alive over the past ten years.