I agree.
When they wanted to do a reunion TV movie for McHale's Navy in the late 70s/ early 80s and they approached Borgnine with the idea he told them "where are you going to find another Joe Flynn?". They knew Borgnine was right and realized without Flynn it would be a waste of time and dropped the idea.
I always thought Flynn should have gotten top billing on MN but Borgnine was better known and had an Oscar. Flynn tended to take over the camera in any scene he was in (one reason he was fired from the Joey Bishop Show a decade earlier).
shareI believe the explanation comes from the way those awards were given out, and from the poor differentiation between lead and supporting actors. Flynn's role was definitely not as the star of the series. Tim Conway really was the second star behind Borgnine.
Yet Conway got a nomination for supporting actor. Ironically, he competed against three actors in one-time performances and against Don Knotts, who truly was a co-star of The Andy Griffith Show, with Knotts winning that year.
A check of the history of the Emmy Awards shows it is riddled with all sorts of people either winning or being nominated in categories that are quite different than where they belong--supporting or lead, I mean.
For some years, actors in comedies had to compete against actors in dramas. In 1960-61, Barbara Hale, Della, from Perry Mason lost out to Knott's Barney Fife. There are two clear ways they should never have been competing for the same award.
Had they truly a list of "supporting" characters in regular roles in comedies, Joe Flynn might well have won. He certainly was one of the funniest supporting characters in any TV series I have ever seen.