Are upsets or struggles vs lesser fighters more likely when champions defend their titles 2 + times?

When a fighter especially a champion fights more they have a greater chance of losing. Even if we take out every single factor you described. I don't think fighting 3 times a year makes a fighter more likely to lose one of those 3 fights then 3 fights stretched out over 3 years. I referenced it earlier today but there was a thread a few months on whether Hearns could have matched Fosters reign where a few posters explained it very well.

What I think matters more is fight time and how difficult each fight was. If a champ fights 3 times and fights 3 or 4 rounds thats 1/4 or 1/3 a full fight. A champion having full fights against the toughest opponents of their reign back to back now that can start to take its toll fast. But that usually doesn't happen. What really matters is how good the opponents are.

While your last point makes sense the other guys who've ruled that long really haven't had "off nights" at least not random ones when they were doing the ruling. They mostly did worse against their tougher opponents.

Upsets and "off nights" are most likely to come in shorter fights like 10 rounders. But champs and top contenders don't really do that anymore. I don't want to count right now but Holmes might have lost Cooney, Witherspoon and Weaver if those were 10 rounders. 12 or 15 rounds gives the better fighter time to make up for getting knocked down or a few bad rounds.