I'm not sure he would. Wasn't Jackson part of one of the readings and brought in because of that? I don't believe he was an original understudy. But, regardless, that is a case of the lead missing opening night.
"If you try to shag my husband while I am still alive, I will shove the art of motorcycle maintenance up your rancid little Cu**. That's a good dear"
Tom Stoppard's Rock N Roll
I wouldn't count Cheyenne in Xanadu, as he was brought in as a replacement, rather than an understudy. James Carpinello never returned to the show after his injury and Cheyenne did pretty much the entire run except for when he took the time off to do Damn Yankees at City Center.
As far as Tony nominations I've always understood the rule to mean that nominations are based on the credits on opening night. So as long as the principal actor is still listed as playing the role in the Playbill then it doesn't matter if the understudy goes on for them or not. The understudy is still billed as the understudy, and the principal actor is still billed as playing said role.
This from Playbill re: the Roundabout's revival of Pal Joey:
"As in showbiz fables of yore, a newcomer is taking over a Broadway lead after a star's injury. Understudy Matthew Risch, according to the actor's spokesperson and the producer, will permanently step into the title role of Pal Joey, replacing Tony Award winner Christian Hoff."
LaChanze was absolutely on for opening night. Tony rules state that eligibility for a Best Performance nomination is determined by the opening night Playbill, in addition to the standard eligibility rules. And LaChanze wasn't only nominated for her Tony - she won that year, in what many consider an upset as Patti LuPone was the favorite amongst many for her performance in Sweeney Todd.
Oh, and not to mention - Ms. Winfrey would have lost her damn mind had her star not been on stage that night. We all saw the wrath that Fantasia suffered (although the situation was much different).
I will say, I saw The Color Purple twice when I lived in NY. Both times, Kenita Miller was on. Not sure what it is about that role that causes Celie to be out so much.