Two thoughts:
1. I can think of at least one time when the replacement received the Tony Nomination. Dean Jones opened in Company in 1970, and left (as I recall) a couple of months later. Larry Kert replaced him and was in the role for a long time when the Tony noms came out. He was nominated for his performance, losing to Hal Linden in The Rothschilds. I seem to recall that win being a big upset at the time, but I always thought that it want to the right person.
I never understood why Kert was deemed eligible -- Jones is even on the original cast recording -- but always assumed that he benefited from being in the role for so long before the Tony noms. The show was a huge critical success, many other performers were nominated (silly that the central role would be disqualified on a technicality), and Tony voters had (I think) 8 or 9 months to see the show between his arrival and the Tonys. (As I recall, it opened late in the prior season that it was open almost a year when the Tony noms came out).
2. Hardly worth the time even thinking about it, since there is no humanly way that he or Pasquale would EVER get nominated for a Tony in this year. We already have a number of people who have gotten reviews ranging from very good to great (not the case with Pasquale, who got mixed reviews): Jeff Daniels, Paddy Considine, Brian Cranston, Daniel Radcliffe, Michael Urie, Ethan Hawke, the lead in Choir Boy (can't remember his name right this second), and still have Tracy Letts, Nathan Lane, John Lithgow, Adam Driver, Bertie Carvel and Johnny Lee Miller to come. It is a moot point but, IMO, would NEVER happen. First of all, Tony voters would all have to see the play again, which ain't gonna happen.